diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 714f75ee7..19f733d7c 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -32,3 +32,7 @@ jobs: repository: ${{ env.GITHUB_REPOSITORY }} env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + release-to-pypi: + uses: deepmodeling/workflows/.github/workflows/release-to-pypi.yml@main + secrets: + PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }} diff --git a/README.md b/README.md index 897cd1cf0..c9bc9494b 100644 --- a/README.md +++ b/README.md @@ -189,6 +189,10 @@ If you want to specify a structure as starting point for `init_bulk`, you may se "from_poscar": true, "from_poscar_path": "....../C_mp-47_conventional.POSCAR", ``` +`init_bulk` support both VASP and ABACUS for first-principle calculation. You can choose the software by specifying the key `init_fp_style`. If `init_fp_style` is not specified, the default software will be VASP. + +When using ABACUS for `init_fp_style`, the keys of the paths of `INPUT` files for relaxation and MD simulations are the same as `INCAR` for VASP, which are `relax_incar` and `md_incar` respectively. You have to additionally specify `relax_kspacing` and `md_kspacing` for k points spacing, and dpgen will automatically generate `KPT` files according to them. You may also use `relax_kpt` and `md_kpt` instead of them for the relative path for `KPT` files of relaxation and MD simulations. However, either `relax_kspacing` and `md_kspacing`, or `relax_kpt` and `md_kpt` is needed. If `from_poscar` is set to `false`, you have to specify `atom_masses` in the same order as `elements`. + The following table gives explicit descriptions on keys in `PARAM`. The bold notation of key (such as **Elements**) means that it's a necessary key. @@ -200,9 +204,9 @@ The bold notation of key (such as **Elements**) means that it's a necessary key. | cell_type | String | "hcp" | Specifying which typical structure to be generated. **Options** include fcc, hcp, bcc, sc, diamond. | latt | Float | 4.479 | Lattice constant for single cell. | from_poscar | Boolean | True | Deciding whether to use a given poscar as the beginning of relaxation. If it's true, keys (`cell_type`, `latt`) will be aborted. Otherwise, these two keys are **necessary**. -| from_poscar_path | String | "....../C_mp-47_conventional.POSCAR" | Path of POSCAR. **Necessary** if `from_poscar` is true. -| relax_incar | String | "....../INCAR" | Path of INCAR for relaxation in VASP. **Necessary** if `stages` include 1. -| md_incar | String | "....../INCAR" | Path of INCAR for MD in VASP. **Necessary** if `stages` include 3.| +| from_poscar_path | String | "....../C_mp-47_conventional.POSCAR" | Path of POSCAR for VASP or STRU for ABACUS. **Necessary** if `from_poscar` is true. +| relax_incar | String | "....../INCAR" | Path of INCAR for VASP or INPUT for ABACUS for relaxation in VASP. **Necessary** if `stages` include 1. +| md_incar | String | "....../INCAR" | Path of INCAR for VASP or INPUT for ABACUS for MD in VASP. **Necessary** if `stages` include 3.| | **scale** | List of float | [0.980, 1.000, 1.020] | Scales for transforming cells. | **skip_relax** | Boolean | False | If it's true, you may directly run stage 2 (pertub and scale) using an unrelaxed POSCAR. | **pert_numb** | Integer | 30 | Number of pertubations for each POSCAR. @@ -211,6 +215,12 @@ The bold notation of key (such as **Elements**) means that it's a necessary key. | **md_nstep** | Integer | 10 | Steps of AIMD in stage 3. If it's not equal to settings via `NSW` in `md_incar`, DP-GEN will follow `NSW`. | **coll_ndata** | Integer | 5000 | Maximal number of collected data. | type_map | List | [ "Mg", "Al"] | The indices of elements in deepmd formats will be set in this order. +| init_fp_style | String | "ABACUS" or "VASP" | First-principle software. If this key is abscent, the default value will be "VASP". +| relax_kpt | String | "....../KPT" | Path of `KPT` file for relaxation in stage 1. Only useful if `init_fp_style` is "ABACUS". +| relax_kspacing | Integer or List of 3 integers | 10 | kspacing parameter for relaxation in stage 1. Only useful if `init_fp_style` is "ABACUS". +| md_kpt | String | "....../KPT" | Path of `KPT` file for MD simulations in stage 3. Only useful if `init_fp_style` is "ABACUS". +| md_kspacing | Integer or List of 3 integers | 10 | kspacing parameter for MD simulations in stage 3. Only useful if `init_fp_style` is "ABACUS". +| atom_masses | List of float | [24] | List of atomic masses of elements. The order should be the same as `Elements`. Only useful if `init_fp_style` is "ABACUS". ### Init_surf diff --git a/doc/conf.py b/doc/conf.py index 4bc4d16d6..f31e2b3eb 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -38,6 +38,7 @@ # ] extensions = [ + 'deepmodeling_sphinx', "sphinx_rtd_theme", 'myst_parser', 'sphinx.ext.autosummary', diff --git a/doc/requirements.txt b/doc/requirements.txt index df6eb698d..e1b2ed852 100644 --- a/doc/requirements.txt +++ b/doc/requirements.txt @@ -3,3 +3,4 @@ recommonmark==0.7.1 sphinx_rtd_theme==0.5.2 sphinx_markdown_tables==0.0.15 myst-parser==0.13.7 +deepmodeling_sphinx diff --git a/dpgen/auto_test/EOS.py b/dpgen/auto_test/EOS.py index 83a7482ab..4f332198b 100644 --- a/dpgen/auto_test/EOS.py +++ b/dpgen/auto_test/EOS.py @@ -169,8 +169,8 @@ def _compute_lower(self, # vol = self.vol_start + ii * self.vol_step vol = loadfn(os.path.join(all_tasks[ii], 'eos.json'))['volume'] task_result = loadfn(all_res[ii]) - res_data[vol] = task_result['energies'][-1] / task_result['atom_numbs'].sum() - ptr_data += '%7.3f %8.4f \n' % (vol, task_result['energies'][-1] / task_result['atom_numbs'].sum()) + res_data[vol] = task_result['energies'][-1] / sum(task_result['atom_numbs']) + ptr_data += '%7.3f %8.4f \n' % (vol, task_result['energies'][-1] / sum(task_result['atom_numbs'])) # res_data[vol] = all_res[ii]['energy'] / len(all_res[ii]['force']) # ptr_data += '%7.3f %8.4f \n' % (vol, all_res[ii]['energy'] / len(all_res[ii]['force'])) diff --git a/dpgen/auto_test/common_equi.py b/dpgen/auto_test/common_equi.py index ce5df94e8..4be84b008 100644 --- a/dpgen/auto_test/common_equi.py +++ b/dpgen/auto_test/common_equi.py @@ -114,46 +114,6 @@ def make_equi(confs, inter.make_input_file(ii, 'relaxation', relax_param) -def worker(work_path, - run_task, - forward_common_files, - forward_files, - backward_files, - mdata, - inter_type): - machine, resources, command, group_size = util.get_machine_info(mdata, inter_type) - disp = make_dispatcher(machine, resources, work_path, [run_task], group_size) - print("%s --> Runing... " % (work_path)) - - api_version = mdata.get('api_version', '0.9') - if LooseVersion(api_version) < LooseVersion('1.0'): - warnings.warn(f"the dpdispatcher will be updated to new version." - f"And the interface may be changed. Please check the documents for more details") - disp.run_jobs(resources, - command, - work_path, - [run_task], - group_size, - forward_common_files, - forward_files, - backward_files, - outlog='outlog', - errlog='errlog') - elif LooseVersion(api_version) >= LooseVersion('1.0'): - submission = make_submission( - mdata_machine=machine, - mdata_resources=resources, - commands=[command], - work_path=work_path, - run_tasks=run_task, - group_size=group_size, - forward_common_files=forward_common_files, - forward_files=forward_files, - backward_files=backward_files, - outlog='outlog', - errlog='errlog' - ) - submission.run_submission() def run_equi(confs, inter_param, @@ -166,18 +126,16 @@ def run_equi(confs, conf_dirs.sort() processes = len(conf_dirs) - pool = Pool(processes=processes) - print("Submit job via %d processes" % processes) # generate a list of task names like mp-xxx/relaxation/relax_task # ... work_path_list = [] for ii in conf_dirs: - work_path_list.append(os.path.abspath(os.path.join(ii, 'relaxation'))) + work_path_list.append(os.path.join(ii, 'relaxation')) all_task = [] for ii in work_path_list: all_task.append(os.path.join(ii, 'relax_task')) - + run_tasks = all_task inter_type = inter_param['type'] # vasp if inter_type == "vasp": @@ -186,7 +144,7 @@ def run_equi(confs, mdata = convert_mdata(mdata, ["model_devi"]) else: raise RuntimeError("unknown task %s, something wrong" % inter_type) - + # dispatch the tasks # POSCAR here is useless virtual_calculator = make_calculator(inter_param, "POSCAR") @@ -194,33 +152,43 @@ def run_equi(confs, forward_common_files = virtual_calculator.forward_common_files() backward_files = virtual_calculator.backward_files() # backward_files += logs - # ... - run_tasks = util.collect_task(all_task, inter_type) - if len(run_tasks) == 0: - return - else: - run_tasks = [os.path.basename(ii) for ii in all_task] - machine, resources, command, group_size = util.get_machine_info(mdata, inter_type) - print('%d tasks will be submited '%len(run_tasks)) - multiple_ret = [] - for ii in range(len(work_path_list)): - work_path = work_path_list[ii] - - ret = pool.apply_async(worker, (work_path, - run_tasks[ii], - forward_common_files, - forward_files, - backward_files, - mdata, - inter_type, - )) - multiple_ret.append(ret) - pool.close() - pool.join() - for ii in range(len(multiple_ret)): - if not multiple_ret[ii].successful(): - raise RuntimeError("Task %d is not successful! work_path: %s " % (ii, work_path_list[ii])) - print('finished') + machine, resources, command, group_size = util.get_machine_info(mdata, inter_type) + work_path = os.getcwd() + print("%s --> Runing... " % (work_path)) + + api_version = mdata.get('api_version', '0.9') + if LooseVersion(api_version) < LooseVersion('1.0'): + warnings.warn(f"the dpdispatcher will be updated to new version." + f"And the interface may be changed. Please check the documents for more details") + disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size) + disp.run_jobs(resources, + command, + work_path, + run_tasks, + group_size, + forward_common_files, + forward_files, + backward_files, + outlog='outlog', + errlog='errlog') + elif LooseVersion(api_version) >= LooseVersion('1.0'): + + submission = make_submission( + mdata_machine=machine, + mdata_resources=resources, + commands=[command], + work_path=work_path, + run_tasks=run_tasks, + group_size=group_size, + forward_common_files=forward_common_files, + forward_files=forward_files, + backward_files=backward_files, + outlog='outlog', + errlog='errlog' + ) + submission.run_submission() + + def post_equi(confs, inter_param): # find all POSCARs and their name like mp-xxx diff --git a/dpgen/auto_test/common_prop.py b/dpgen/auto_test/common_prop.py index bda655cf3..6bc7d9241 100644 --- a/dpgen/auto_test/common_prop.py +++ b/dpgen/auto_test/common_prop.py @@ -173,6 +173,7 @@ def run_property(confs, pool.join() for ii in range(len(multiple_ret)): if not multiple_ret[ii].successful(): + print("ERROR:", multiple_ret[ii].get()) raise RuntimeError("Job %d is not successful!" % ii) print('%d jobs are finished' % len(multiple_ret)) @@ -186,11 +187,11 @@ def worker(work_path, inter_type): run_tasks = [os.path.basename(ii) for ii in all_task] machine, resources, command, group_size = util.get_machine_info(mdata, inter_type) - disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size) api_version = mdata.get('api_version', '0.9') if LooseVersion(api_version) < LooseVersion('1.0'): warnings.warn(f"the dpdispatcher will be updated to new version." f"And the interface may be changed. Please check the documents for more details") + disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size) disp.run_jobs(resources, command, work_path, diff --git a/dpgen/auto_test/lib/lammps.py b/dpgen/auto_test/lib/lammps.py index 9b2820ffa..a1c225e95 100644 --- a/dpgen/auto_test/lib/lammps.py +++ b/dpgen/auto_test/lib/lammps.py @@ -241,6 +241,8 @@ def make_lammps_equi(conf, type_map, interaction, param, ret += "fix 1 all box/relax iso 0.0 \n" ret += "minimize %e %e %d %d\n" % (etol, ftol, maxiter, maxeval) ret += "fix 1 all box/relax aniso 0.0 \n" + ret += "minimize %e %e %d %d\n" % (etol, ftol, maxiter, maxeval) + ret += "fix 1 all box/relax tri 0.0 \n" ret += "minimize %e %e %d %d\n" % (etol, ftol, maxiter, maxeval) ret += "variable N equal count(all)\n" ret += "variable V equal vol\n" diff --git a/dpgen/data/gen.py b/dpgen/data/gen.py index 842752b88..b14034c1d 100644 --- a/dpgen/data/gen.py +++ b/dpgen/data/gen.py @@ -23,6 +23,8 @@ from distutils.version import LooseVersion from dpgen.generator.lib.vasp import incar_upper from dpgen.generator.lib.utils import symlink_user_forward_files +from dpgen.generator.lib.abacus_scf import get_abacus_input_parameters, get_abacus_STRU, make_supercell_abacus, make_abacus_scf_stru\ + , make_kspacing_kpoints_stru, make_abacus_scf_kpt from pymatgen.core import Structure from pymatgen.io.vasp import Incar from dpgen.remote.decide_machine import convert_mdata @@ -127,6 +129,23 @@ def poscar_ele(poscar_in, poscar_out, eles, natoms) : with open(poscar_out, 'w') as fout : fout.write("".join(lines)) +def stru_ele(supercell_stru, stru_out, eles, natoms, jdata, path_work): + supercell_stru["types"] = [] + supercell_stru["atom_numbs"] = list(natoms) + for iele in range(len(natoms)): + for iatom in range(natoms[iele]): + supercell_stru["types"].append(iele) + pp_file_names = [os.path.basename(a) for a in jdata['potcars']] + supercell_stru["atom_masses"] = jdata["atom_masses"] + supercell_stru["atom_names"] = eles + stru_text = make_abacus_scf_stru(supercell_stru, pp_file_names) + with open(stru_out, "w") as f: + f.write(stru_text) + absolute_pp_file_path = [os.path.abspath(a) for a in jdata["potcars"]] + for ipp, pp_file in enumerate(absolute_pp_file_path): + os.symlink(pp_file, os.path.join(path_work, pp_file_names[ipp])) + + def poscar_natoms(lines) : numb_atoms = 0 for ii in lines[6].split() : @@ -145,6 +164,17 @@ def poscar_shuffle(poscar_in, poscar_out) : with open(poscar_out, 'w') as fout: fout.write("".join(out_lines)) +def shuffle_stru_data(supercell_stru): + atom_numb = sum(supercell_stru["atom_numbs"]) + assert(np.shape(supercell_stru["coords"]) == (atom_numb, 3)) + new_coord = np.zeros([atom_numb, 3]) + order = np.arange(0, atom_numb) + np.random.shuffle(order) + for idx in range(atom_numb): + new_coord[idx] = supercell_stru["coords"][order[idx]] + supercell_stru['coords'] = new_coord + return supercell_stru + def poscar_scale_direct (str_in, scale) : lines = str_in.copy() numb_atoms = poscar_natoms(lines) @@ -182,6 +212,16 @@ def poscar_scale (poscar_in, poscar_out, scale) : with open(poscar_out, 'w') as fout: fout.write("".join(lines)) +def poscar_scale_abacus(poscar_in, poscar_out, scale, jdata): + stru = get_abacus_STRU(poscar_in, n_ele=len(jdata["elements"])) + stru["cells"] *= scale + stru["coords"] *= scale + pp_files = [os.path.basename(a) for a in jdata['potcars']] + ret = make_abacus_scf_stru(stru, pp_files) + with open(poscar_out, "w") as fp: + fp.write(ret) + + def make_unit_cell (jdata) : latt = jdata['latt'] out_dir = jdata['out_dir'] @@ -197,6 +237,24 @@ def make_unit_cell (jdata) : fp.write (cell_type.poscar_unit(latt)) os.chdir(cwd) +def make_unit_cell_ABACUS (jdata) : + latt = jdata['latt'] + out_dir = jdata['out_dir'] + path_uc = os.path.join(out_dir, global_dirname_02) + cell_type = class_cell_type(jdata) + cwd = os.getcwd() + path_work = create_path(path_uc) + os.chdir(path_work) + with open('POSCAR.unit', 'w') as fp: + fp.write (cell_type.poscar_unit(latt)) + stru_data = dpdata.System("POSCAR.unit", fmt = 'vasp/poscar').data + os.chdir(cwd) + stru_data['coords'] = np.squeeze(stru_data['coords']) + stru_data['cells'] = np.squeeze(stru_data['cells']) + del stru_data["atom_names"] + return stru_data + + def make_super_cell (jdata) : out_dir = jdata['out_dir'] super_cell = jdata['super_cell'] @@ -216,6 +274,28 @@ def make_super_cell (jdata) : from_struct.make_supercell(super_cell) from_struct.to('poscar',to_file) +def make_super_cell_ABACUS (jdata, stru_data) : + out_dir = jdata['out_dir'] + super_cell = jdata['super_cell'] + path_uc = os.path.join(out_dir, global_dirname_02) + path_sc = os.path.join(out_dir, global_dirname_02) + assert(os.path.isdir(path_uc)), "path %s should exists" % path_uc + assert(os.path.isdir(path_sc)), "path %s should exists" % path_sc + + # for ii in scale : + #from_path = path_uc + #from_file = os.path.join(from_path, 'POSCAR.unit') + #to_path = path_sc + #to_file = os.path.join(to_path, 'POSCAR') + + #minor bug for element symbol behind the coordinates + #from_struct=Structure.from_file(from_file) + #from_struct.make_supercell(super_cell) + #from_struct.to('poscar',to_file) + supercell_stru = make_supercell_abacus(stru_data, super_cell) + return supercell_stru + + def make_super_cell_poscar(jdata) : out_dir = jdata['out_dir'] super_cell = jdata['super_cell'] @@ -255,6 +335,53 @@ def make_super_cell_poscar(jdata) : pass os.chdir(cwd) +def make_super_cell_STRU(jdata) : + out_dir = jdata['out_dir'] + super_cell = jdata['super_cell'] + path_sc = os.path.join(out_dir, global_dirname_02) + create_path(path_sc) + from_poscar_path = jdata['from_poscar_path'] + assert(os.path.isfile(from_poscar_path)), "file %s should exists" % from_poscar_path + + from_file = os.path.join(path_sc, 'STRU.copied') + shutil.copy2(from_poscar_path, from_file) + to_path = path_sc + to_file = os.path.join(to_path, 'STRU') + + from_struct=get_abacus_STRU(from_file, n_ele=len(jdata["elements"])) + from_struct = make_supercell_abacus(from_struct, super_cell) + pp_file_names = [os.path.basename(a) for a in jdata['potcars']] + stru_text = make_abacus_scf_stru(from_struct, pp_file_names) + with open(to_file, "w") as fp: + fp.write(stru_text) + # if kspacing is specified in json file, use kspacing to generate KPT (rather than directly using specified KPT). + if 'relax_kspacing' in jdata: + kpoints = make_kspacing_kpoints_stru(from_struct, jdata['relax_kspacing']) + kpt_text = make_abacus_scf_kpt({"k_points": kpoints}) + with open(os.path.join(to_path, 'KPT'), "w") as fp: + fp.write(kpt_text) + # make system dir (copy) + natoms_list = from_struct['atom_numbs'] + dlog.info(natoms_list) + comb_name = "sys-" + for idx,ii in enumerate(natoms_list) : + comb_name += "%04d" % ii + if idx != len(natoms_list)-1 : + comb_name += "-" + path_work = os.path.join(path_sc, comb_name) + create_path(path_work) + cwd = os.getcwd() + absolute_pp_file_path = [os.path.abspath(a) for a in jdata['potcars']] + to_file = os.path.abspath(to_file) + os.chdir(path_work) + try: + os.symlink(os.path.relpath(to_file), 'STRU') + for ipp, pp_file in enumerate(absolute_pp_file_path): + os.symlink(pp_file, pp_file_names[ipp]) # create pseudo-potential files + except FileExistsError: + pass + os.chdir(cwd) + def make_combines (dim, natoms) : if dim == 1 : return [[natoms]] @@ -299,6 +426,40 @@ def place_element (jdata) : poscar_ele(pos_in, pos_out, elements, ii) poscar_shuffle(pos_out, pos_out) +def place_element_ABACUS(jdata, supercell_stru): + out_dir = jdata['out_dir'] + super_cell = jdata['super_cell'] + cell_type = class_cell_type(jdata) + natoms = sum(supercell_stru['atom_numbs']) + elements = jdata['elements'] + #path_sc = os.path.join(out_dir, global_dirname_02) + path_pe = os.path.join(out_dir, global_dirname_02) + combines = np.array(make_combines(len(elements), natoms), dtype = int) + # if kspacing is specified in json file, use kspacing to generate KPT (rather than directly using specified KPT). + if 'relax_kspacing' in jdata: + kpoints = make_kspacing_kpoints_stru(supercell_stru) + kpt_text = make_abacus_scf_kpt({"k_points": kpoints}) + with open(os.path.join(path_pe, 'KPT')) as fp: + fp.write(kpt_text) + assert(os.path.isdir(path_pe)) + cwd = os.getcwd() + for ii in combines : + if any(ii == 0) : + continue + comb_name = "sys-" + for idx,jj in enumerate(ii) : + comb_name += "%04d" % jj + if idx != len(ii)-1 : + comb_name += "-" + #path_pos_in = path_sc + path_work = os.path.join(path_pe, comb_name) + create_path(path_work) + #pos_in = os.path.join(path_pos_in, 'POSCAR') + pos_out = os.path.join(path_work, 'STRU') + supercell_stru = shuffle_stru_data(supercell_stru) + stru_ele(supercell_stru, pos_out, elements, ii, jdata, path_work) + + def make_vasp_relax (jdata, mdata) : out_dir = jdata['out_dir'] potcars = jdata['potcars'] @@ -347,6 +508,45 @@ def make_vasp_relax (jdata, mdata) : work_path=os.path.join(os.path.basename(out_dir),global_dirname_02), task_format= {"fp" : "sys-*"}) +def make_abacus_relax (jdata, mdata) : + out_dir = jdata['out_dir'] + cwd = os.getcwd() + work_dir = os.path.join(out_dir, global_dirname_02) + assert (os.path.isdir(work_dir)) + work_dir = os.path.abspath(work_dir) + + if os.path.isfile(os.path.join(work_dir, 'INPUT' )) : + os.remove(os.path.join(work_dir, 'INPUT' )) + shutil.copy2( jdata['relax_incar'], + os.path.join(work_dir, 'INPUT')) + + if 'relax_kspacing' not in jdata: + if os.path.isfile(os.path.join(work_dir, 'KPT' )) : + os.remove(os.path.join(work_dir, 'KPT' )) + assert('relax_kpt' in jdata) + #print(jdata['relax_kpt']) + jdata['relax_kpt'] = os.path.relpath(jdata['relax_kpt']) + shutil.copy2( jdata['relax_kpt'], + os.path.join(work_dir, 'KPT')) + + os.chdir(work_dir) + + sys_list = glob.glob('sys-*') + for ss in sys_list: + os.chdir(ss) + ln_src = os.path.relpath(os.path.join(work_dir,'INPUT')) + kpt_src = os.path.relpath(os.path.join(work_dir,'KPT')) + try: + os.symlink(ln_src, 'INPUT') + os.symlink(kpt_src, 'KPT') + except FileExistsError: + pass + os.chdir(work_dir) + os.chdir(cwd) + symlink_user_forward_files(mdata=mdata, task_type="fp", + work_path=os.path.join(os.path.basename(out_dir),global_dirname_02), + task_format= {"fp" : "sys-*"}) + def make_scale(jdata): out_dir = jdata['out_dir'] scale = jdata['scale'] @@ -379,14 +579,51 @@ def make_scale(jdata): os.chdir(scale_path) poscar_scale(pos_src, 'POSCAR', jj) os.chdir(cwd) - + +def make_scale_ABACUS(jdata): + out_dir = jdata['out_dir'] + scale = jdata['scale'] + skip_relax = jdata['skip_relax'] + + cwd = os.getcwd() + init_path = os.path.join(out_dir, global_dirname_02) + init_path = os.path.abspath(init_path) + work_path = os.path.join(out_dir, global_dirname_03) + os.chdir(init_path) + init_sys = glob.glob("sys-*") + init_sys.sort() + os.chdir(cwd) + + create_path(work_path) + for ii in init_sys : + for jj in scale : + if skip_relax : + pos_src = os.path.join(os.path.join(init_path, ii), 'STRU') + assert(os.path.isfile(pos_src)) + else : + try: + pos_src = os.path.join(os.path.join(init_path, ii), 'OUT.ABACUS/STRU_ION_D') + assert(os.path.isfile(pos_src)) + except: + raise RuntimeError("not file %s, vasp relaxation should be run before scale poscar") + scale_path = os.path.join(work_path, ii) + scale_path = os.path.join(scale_path, "scale-%.3f" % jj) + create_path(scale_path) + os.chdir(scale_path) + poscar_scale_abacus(pos_src, 'STRU', jj, jdata) + os.chdir(cwd) + + def pert_scaled(jdata) : + if "init_fp_style" not in jdata: + jdata["init_fp_style"] = "VASP" out_dir = jdata['out_dir'] scale = jdata['scale'] pert_box = jdata['pert_box'] pert_atom = jdata['pert_atom'] pert_numb = jdata['pert_numb'] + pp_file = [os.path.basename(a) for a in jdata['potcars']] from_poscar = False if 'from_poscar' in jdata : from_poscar = jdata['from_poscar'] @@ -402,7 +639,12 @@ def pert_scaled(jdata) : pert_cmd = os.path.dirname(__file__) pert_cmd = os.path.join(pert_cmd, 'tools') pert_cmd = os.path.join(pert_cmd, 'create_random_disturb.py') - pert_cmd = 'python3 ' + pert_cmd + ' -etmax %f -ofmt vasp POSCAR %d %f > /dev/null' %(pert_box, pert_numb, pert_atom) + fp_style = "vasp" + poscar_name = "POSCAR" + if jdata['init_fp_style'] == "ABACUS": + fp_style = "abacus" + poscar_name = "STRU" + pert_cmd = 'python3 ' + pert_cmd + ' -etmax %f -ofmt %s %s %d %f > /dev/null' %(pert_box, fp_style, poscar_name, pert_numb, pert_atom) for ii in sys_pe : for jj in scale : path_work = path_sp @@ -412,22 +654,46 @@ def pert_scaled(jdata) : os.chdir(path_work) sp.check_call(pert_cmd, shell = True) for kk in range(pert_numb) : - pos_in = 'POSCAR%d.vasp' % (kk+1) + if fp_style == "vasp": + pos_in = 'POSCAR%d.vasp' % (kk+1) + elif fp_style == "abacus": + pos_in = 'STRU%d.abacus' % (kk+1) dir_out = '%06d' % (kk+1) create_path(dir_out) - pos_out = os.path.join(dir_out, 'POSCAR') + if fp_style == "vasp": + pos_out = os.path.join(dir_out, 'POSCAR') + elif fp_style == "abacus": + pos_out = os.path.join(dir_out, 'STRU') if not from_poscar: - poscar_shuffle(pos_in, pos_out) + if fp_style == "vasp": + poscar_shuffle(pos_in, pos_out) + elif fp_style == "abacus": + stru_in = get_abacus_STRU(pos_in) + stru_out = shuffle_stru_data(stru_in) + with open(pos_out, "w") as fp: + fp.write(make_abacus_scf_stru(stru_out, pp_file)) else : shutil.copy2(pos_in, pos_out) os.remove(pos_in) kk = -1 - pos_in = 'POSCAR' + if fp_style == "vasp": + pos_in = 'POSCAR' + elif fp_style == "abacus": + pos_in = 'STRU' dir_out = '%06d' % (kk+1) create_path(dir_out) - pos_out = os.path.join(dir_out, 'POSCAR') + if fp_style == "vasp": + pos_out = os.path.join(dir_out, 'POSCAR') + elif fp_style == "abacus": + pos_out = os.path.join(dir_out, 'STRU') if not from_poscar: - poscar_shuffle(pos_in, pos_out) + if fp_style == "vasp": + poscar_shuffle(pos_in, pos_out) + elif fp_style == "abacus": + stru_in = get_abacus_STRU(pos_in) + stru_out = shuffle_stru_data(stru_in) + with open(pos_out, "w") as fp: + fp.write(make_abacus_scf_stru(stru_out, pp_file)) else : shutil.copy2(pos_in, pos_out) os.chdir(cwd) @@ -500,7 +766,78 @@ def make_vasp_md(jdata, mdata) : symlink_user_forward_files(mdata=mdata, task_type="fp", work_path=os.path.join(os.path.basename(out_dir),global_dirname_04), task_format= {"fp" :"sys-*/scale*/00*"}) - + +def make_abacus_md(jdata, mdata) : + out_dir = jdata['out_dir'] + potcars = jdata['potcars'] + scale = jdata['scale'] + pert_numb = jdata['pert_numb'] + md_nstep = jdata['md_nstep'] + + cwd = os.getcwd() + path_ps = os.path.join(out_dir, global_dirname_03) + path_ps = os.path.abspath(path_ps) + assert(os.path.isdir(path_ps)) + os.chdir(path_ps) + sys_ps = glob.glob('sys-*') + sys_ps.sort() + os.chdir(cwd) + path_md = os.path.join(out_dir, global_dirname_04) + path_md = os.path.abspath(path_md) + create_path(path_md) + shutil.copy2(jdata['md_incar'], + os.path.join(path_md, 'INPUT')) + if 'md_kpt' in jdata: + shutil.copy2(jdata['md_kpt'], + os.path.join(path_md, 'KPT')) + for pp_file in jdata['potcars']: + shutil.copy2(pp_file, + os.path.join(path_md, os.path.basename(pp_file))) + os.chdir(path_md) + os.chdir(cwd) + + + + for ii in sys_ps : + for jj in scale : + for kk in range(pert_numb+1) : + path_work = path_md + path_work = os.path.join(path_work, ii) + path_work = os.path.join(path_work, "scale-%.3f" % jj) + path_work = os.path.join(path_work, "%06d" % kk) + create_path(path_work) + os.chdir(path_work) + path_pos = path_ps + path_pos = os.path.join(path_pos, ii) + path_pos = os.path.join(path_pos, "scale-%.3f" % jj) + path_pos = os.path.join(path_pos, "%06d" % kk) + init_pos = os.path.join(path_pos, 'STRU') + if "md_kspacing" in jdata: + init_stru = get_abacus_STRU(init_pos) + kpoints = make_kspacing_kpoints_stru(init_stru, jdata['md_kspacing']) + kpt_text = make_abacus_scf_kpt({"k_points": kpoints}) + with open(os.path.join(path_md, 'KPT'), "w") as fp: + fp.write(kpt_text) + shutil.copy2 (init_pos, 'STRU') + file_incar = os.path.join(path_md, 'INPUT') + file_kpt = os.path.join(path_md, 'KPT') + try: + os.symlink(os.path.relpath(file_incar), 'INPUT') + os.symlink(os.path.relpath(file_kpt), 'KPT') + except FileExistsError: + pass + try: + for pp_file in [os.path.basename(a) for a in jdata['potcars']]: + os.symlink(os.path.relpath(os.path.join(path_md, pp_file)), pp_file) + except FileExistsError: + pass + + os.chdir(cwd) + + symlink_user_forward_files(mdata=mdata, task_type="fp", + work_path=os.path.join(os.path.basename(out_dir),global_dirname_04), + task_format= {"fp" :"sys-*/scale*/00*"}) + def coll_vasp_md(jdata) : out_dir = jdata['out_dir'] @@ -638,6 +975,127 @@ def run_vasp_relax(jdata, mdata): errlog = 'fp.log') submission.run_submission() +def coll_abacus_md(jdata) : + out_dir = jdata['out_dir'] + md_nstep = jdata['md_nstep'] + scale = jdata['scale'] + pert_numb = jdata['pert_numb'] + coll_ndata = jdata['coll_ndata'] + + cwd = os.getcwd() + path_md = os.path.join(out_dir, global_dirname_04) + path_md = os.path.abspath(path_md) + assert(os.path.isdir(path_md)), "md path should exists" + os.chdir(path_md) + sys_md = glob.glob('sys-*') + sys_md.sort() + + for ii in sys_md : + os.chdir(ii) + # convert outcars + valid_outcars = [] + for jj in scale : + for kk in range(pert_numb+1) : + path_work = os.path.join("scale-%.3f" % jj, "%06d" % kk) + print("path_work = %s" %path_work) + #outcar = os.path.join(path_work, 'OUT.ABACUS/') + outcar = path_work + #dlog.info("OUTCAR",outcar) + if os.path.exists(os.path.join(outcar, "OUT.ABACUS/running_md.log")) : + with open(os.path.join(outcar, "OUT.ABACUS/running_md.log")) as fp: + if "!FINAL_ETOT_IS" in fp.read(): + valid_outcars.append(outcar) + print(outcar) + else: + dlog.info("WARNING : file %s does not have !FINAL_ETOT_IS note. MD simulation is not completed normally."%os.path.join(outcar, "OUT.ABACUS/running_md.log")) + else: + dlog.info("WARNING : in directory %s NO running_md.log file found."%(os.getcwd())) + arg_cvt = " " + if len(valid_outcars) == 0: + raise RuntimeError("MD dir: %s: find no valid OUT.ABACUS in sys %s, " + "check if your abacus md simulation is correctly done." + % (path_md, ii)) + + flag=True + if ("type_map" in jdata) and isinstance(jdata["type_map"], list): + type_map = jdata["type_map"] + else: + type_map = None + for oo in valid_outcars : + if flag: + _sys = dpdata.LabeledSystem(oo, type_map= type_map, fmt='abacus/md') + if len(_sys)>0: + all_sys=_sys + flag=False + else: + pass + else: + _sys = dpdata.LabeledSystem(oo, type_map= type_map, fmt='abacus/md') + if len(_sys)>0: + all_sys.append(_sys) + # create deepmd data + if all_sys.get_nframes() >= coll_ndata : + all_sys = all_sys.sub_system(np.arange(coll_ndata)) + print(all_sys.get_nframes()) + all_sys.to_deepmd_raw('deepmd') + all_sys.to_deepmd_npy('deepmd', set_size = all_sys.get_nframes()) + os.chdir(path_md) + os.chdir(cwd) + +def run_abacus_relax(jdata, mdata): + fp_command = mdata['fp_command'] + fp_group_size = mdata['fp_group_size'] + fp_resources = mdata['fp_resources'] + #machine_type = mdata['fp_machine']['machine_type'] + work_dir = os.path.join(jdata['out_dir'], global_dirname_02) + pp_files = [os.path.basename(a) for a in jdata["potcars"]] + forward_files = ["STRU", "INPUT", "KPT"] + pp_files + user_forward_files = mdata.get("fp" + "_user_forward_files", []) + forward_files += [os.path.basename(file) for file in user_forward_files] + backward_files = ["OUT.ABACUS"] + backward_files += mdata.get("fp" + "_user_backward_files", []) + forward_common_files = [] + relax_tasks = glob.glob(os.path.join(work_dir, "sys-*")) + relax_tasks.sort() + #dlog.info("work_dir",work_dir) + #dlog.info("relax_tasks",relax_tasks) + if len(relax_tasks) == 0: + return + + relax_run_tasks = relax_tasks + #for ii in relax_tasks : + # if not _vasp_check_fin(ii): + # relax_run_tasks.append(ii) + run_tasks = [os.path.basename(ii) for ii in relax_run_tasks] + + api_version = mdata.get('api_version', '0.9') + if LooseVersion(api_version) < LooseVersion('1.0'): + warnings.warn(f"the dpdispatcher will be updated to new version." + f"And the interface may be changed. Please check the documents for more details") + dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size) + dispatcher.run_jobs(fp_resources, + [fp_command], + work_dir, + run_tasks, + fp_group_size, + forward_common_files, + forward_files, + backward_files) + + elif LooseVersion(api_version) >= LooseVersion('1.0'): + submission = make_submission( + mdata['fp_machine'], + mdata['fp_resources'], + commands=[fp_command], + work_path=work_dir, + run_tasks=run_tasks, + group_size=fp_group_size, + forward_common_files=forward_common_files, + forward_files=forward_files, + backward_files=backward_files, + outlog = 'fp.log', + errlog = 'fp.log') + submission.run_submission() def run_vasp_md(jdata, mdata): fp_command = mdata['fp_command'] @@ -706,6 +1164,72 @@ def run_vasp_md(jdata, mdata): errlog = 'fp.log') submission.run_submission() +def run_abacus_md(jdata, mdata): + fp_command = mdata['fp_command'] + fp_group_size = mdata['fp_group_size'] + fp_resources = mdata['fp_resources'] + #machine_type = mdata['fp_machine']['machine_type'] + work_dir = os.path.join(jdata['out_dir'], global_dirname_04) + scale = jdata['scale'] + pert_numb = jdata['pert_numb'] + md_nstep = jdata['md_nstep'] + + forward_files = ["STRU", "INPUT", "KPT"] + for pp_file in [os.path.basename(a) for a in jdata['potcars']]: + forward_files.append(pp_file) + user_forward_files = mdata.get("fp" + "_user_forward_files", []) + forward_files += [os.path.basename(file) for file in user_forward_files] + backward_files = ["OUT.ABACUS"] + backward_files += mdata.get("fp" + "_user_backward_files", []) + forward_common_files = [] + + path_md = work_dir + path_md = os.path.abspath(path_md) + cwd = os.getcwd() + assert(os.path.isdir(path_md)), "md path should exists" + md_tasks = glob.glob(os.path.join(work_dir, 'sys-*/scale*/00*')) + md_tasks.sort() + + if len(md_tasks) == 0: + return + + md_run_tasks = md_tasks + #for ii in md_tasks : + # if not _vasp_check_fin(ii): + # md_run_tasks.append(ii) + + run_tasks = [ii.replace(work_dir+"/", "") for ii in md_run_tasks] + #dlog.info("md_work_dir", work_dir) + #dlog.info("run_tasks",run_tasks) + api_version = mdata.get('api_version', '0.9') + if LooseVersion(api_version) < LooseVersion('1.0'): + warnings.warn(f"the dpdispatcher will be updated to new version." + f"And the interface may be changed. Please check the documents for more details") + dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size) + dispatcher.run_jobs(fp_resources, + [fp_command], + work_dir, + run_tasks, + fp_group_size, + forward_common_files, + forward_files, + backward_files) + + elif LooseVersion(api_version) >= LooseVersion('1.0'): + submission = make_submission( + mdata['fp_machine'], + mdata['fp_resources'], + commands=[fp_command], + work_path=work_dir, + run_tasks=run_tasks, + group_size=fp_group_size, + forward_common_files=forward_common_files, + forward_files=forward_files, + backward_files=backward_files, + outlog = 'fp.log', + errlog = 'fp.log') + submission.run_submission() + def gen_init_bulk(args) : try: import ruamel @@ -736,16 +1260,29 @@ def gen_init_bulk(args) : from_poscar = jdata['from_poscar'] # Verify md_nstep md_nstep_jdata = jdata["md_nstep"] + if 'init_fp_style' not in jdata: + jdata['init_fp_style'] = "VASP" try: md_incar = jdata['md_incar'] if os.path.isfile(md_incar): - standard_incar = incar_upper(Incar.from_file(md_incar)) - nsw_flag = False - if "NSW" in standard_incar: - nsw_flag = True - nsw_steps = standard_incar['NSW'] - #dlog.info("nsw_steps is", nsw_steps) - #dlog.info("md_nstep_jdata is", md_nstep_jdata) + if jdata['init_fp_style'] == "VASP": + standard_incar = incar_upper(Incar.from_file(md_incar)) + nsw_flag = False + if "NSW" in standard_incar: + nsw_flag = True + nsw_steps = standard_incar['NSW'] + #dlog.info("nsw_steps is", nsw_steps) + #dlog.info("md_nstep_jdata is", md_nstep_jdata) + elif jdata['init_fp_style'] == "ABACUS": + standard_incar = get_abacus_input_parameters(md_incar) # a dictionary in which all of the values are strings + nsw_flag = False + if "nstep" in standard_incar: + nsw_flag = True + nsw_steps = int(standard_incar['nstep']) + assert("relax_kpt" in jdata or "relax_kspacing" in jdata) + if 3 in jdata["stages"]: + assert("md_kpt" in jdata or "md_kspacing" in jdata) + assert("md_incar" in jdata) if nsw_flag: if (nsw_steps != md_nstep_jdata): dlog.info("WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!") @@ -771,31 +1308,60 @@ def gen_init_bulk(args) : shutil.copy2(args.PARAM, os.path.join(out_dir, 'param.json')) skip_relax = jdata['skip_relax'] if from_poscar : - make_super_cell_poscar(jdata) + if jdata['init_fp_style'] == "VASP": + make_super_cell_poscar(jdata) + elif jdata['init_fp_style'] == "ABACUS": + make_super_cell_STRU(jdata) else : - make_unit_cell(jdata) - make_super_cell(jdata) - place_element(jdata) - if args.MACHINE is not None and not skip_relax: - make_vasp_relax(jdata, mdata) - run_vasp_relax(jdata, mdata) + if jdata['init_fp_style'] == "VASP": + make_unit_cell(jdata) + make_super_cell(jdata) + place_element(jdata) + elif jdata['init_fp_style'] == "ABACUS": + stru_data = make_unit_cell_ABACUS(jdata) + supercell_stru = make_super_cell_ABACUS(jdata, stru_data) + place_element_ABACUS(jdata, supercell_stru) + if args.MACHINE is not None: + if jdata['init_fp_style'] == "VASP": + make_vasp_relax(jdata, mdata) + run_vasp_relax(jdata, mdata) + elif jdata['init_fp_style'] == "ABACUS": + make_abacus_relax(jdata, mdata) + run_abacus_relax(jdata, mdata) else: - make_vasp_relax(jdata, {"fp_resources":{}}) + if jdata['init_fp_style'] == "VASP": + make_vasp_relax(jdata, {"fp_resources":{}}) + elif jdata['init_fp_style'] == "ABACUS": + make_abacus_relax(jdata, {"fp_resources":{}}) elif stage == 2 : dlog.info("Current stage is 2, perturb and scale") - make_scale(jdata) - pert_scaled(jdata) + if jdata['init_fp_style'] == "VASP": + make_scale(jdata) + pert_scaled(jdata) + elif jdata['init_fp_style'] == "ABACUS": + make_scale_ABACUS(jdata) + pert_scaled(jdata) elif stage == 3 : dlog.info("Current stage is 3, run a short md") if args.MACHINE is not None: - make_vasp_md(jdata, mdata) - run_vasp_md(jdata, mdata) + if jdata['init_fp_style'] == "VASP": + make_vasp_md(jdata, mdata) + run_vasp_md(jdata, mdata) + elif jdata['init_fp_style'] == "ABACUS": + make_abacus_md(jdata, mdata) + run_abacus_md(jdata, mdata) else: - make_vasp_md(jdata, {"fp_resources":{}}) + if jdata['init_fp_style'] == "VASP": + make_vasp_md(jdata, {"fp_resources":{}}) + elif jdata['init_fp_style'] == "ABACUS": + make_abacus_md(jdata, {"fp_resources":{}}) elif stage == 4 : dlog.info("Current stage is 4, collect data") - coll_vasp_md(jdata) + if jdata['init_fp_style'] == "VASP": + coll_vasp_md(jdata) + elif jdata['init_fp_style'] == "ABACUS": + coll_abacus_md(jdata) else : raise RuntimeError("unknown stage %d" % stage) diff --git a/dpgen/data/tools/bcc.py b/dpgen/data/tools/bcc.py index e02483b32..fb96333d5 100644 --- a/dpgen/data/tools/bcc.py +++ b/dpgen/data/tools/bcc.py @@ -20,4 +20,3 @@ def poscar_unit (latt) : ret += "%.16f %.16f %.16f\n" % (0.0, 0.0, 0.0) ret += "%.16f %.16f %.16f\n" % (0.5, 0.5, 0.5) return ret - diff --git a/dpgen/data/tools/create_random_disturb.py b/dpgen/data/tools/create_random_disturb.py index 728b8ddf5..542a16096 100755 --- a/dpgen/data/tools/create_random_disturb.py +++ b/dpgen/data/tools/create_random_disturb.py @@ -10,6 +10,7 @@ import ase.io import io_lammps +from dpgen.generator.lib.abacus_scf import get_abacus_STRU, make_abacus_scf_stru def create_disturbs_atomsk(fin, nfile, dmax=1.0, ofmt="lmp"): # removing the exists files @@ -164,6 +165,68 @@ def create_disturbs_ase_dev(fin, nfile, dmax=1.0, etmax=0.1, ofmt="lmp", dstyle= fw.close() return +def create_disturbs_abacus_dev(fin, nfile, dmax=1.0, etmax=0.1, ofmt="abacus", dstyle='uniform', write_d=False, diag=0): + # removing the exists files + flist = glob.glob('*.' + ofmt) + for f in flist: + os.remove(f) + + # read-in by ase + #atoms = ase.io.read(fin) + #natoms = atoms.get_number_of_atoms() + #cell0 = atoms.get_cell() + + stru = get_abacus_STRU(fin) + natoms = sum(stru["atom_numbs"]) + cell0 = stru['cells'] + + # creat nfile ofmt files. + for fid in range(1, nfile + 1): + # Use copy(), otherwise it will modify the input atoms every time. + stru_d = stru.copy() + + # random flux for atomic positions + if write_d: + fw = open('disp-' + str(fid) + '.dat', 'w') + dpos = np.zeros((natoms, 3)) + for i in range(natoms): + dr = gen_random_disturb(dmax, -0.5, 0.5, dstyle) + dpos[i, :] = dr + if write_d: + dnorm = np.linalg.norm(dr) + fw.write('%d\t%f\t%f\t%f\t%f\n' % + (i + 1, dr[0], dr[1], dr[2], dnorm)) + fw.flush() + + # random flux for volumes + cell = np.dot(cell0, gen_random_emat(etmax, diag)) + stru_d['cells'] = cell + if write_d: + fout_c = 'cell-' + str(fid) + '.dat' + np.savetxt(fout_c, cell, '%f') + + # determine new cell & atomic positions randomiziations + stru_d['coords'] += dpos + + # pre-converting the Atoms to be in low tri-angular cell matrix + cell_new = io_lammps.convert_cell(cell) + #pos_new = io_lammps.convert_positions(pos, cell, cell_new) + stru_d['cells'] = cell_new + + convert_mat = np.linalg.inv(cell)*cell_new + stru_d['coords'] = np.matmul(stru_d['coords'], convert_mat) + + + # Writing it + fout = fin + str(fid) + '.' + ofmt + print("Creating %s ..." % fout) + ret = make_abacus_scf_stru(stru_d, stru_d['pp_files']) + with open(fout, "w") as fp: + fp.write(ret) + if write_d: + fw.close() + return + def create_random_alloys(fin, alloy_dist, ifmt='vasp', ofmt='vasp'): ''' @@ -252,5 +315,9 @@ def RandomDisturbParser(): # main program #create_disturbs_atomsk(fin, nfile, dmax, ofmt) #create_disturbs_ase(fin, nfile, dmax, ofmt, dstyle, write_d) - create_disturbs_ase_dev(fin, nfile, dmax, etmax, + if ofmt == "vasp": + create_disturbs_ase_dev(fin, nfile, dmax, etmax, ofmt, dstyle, write_d, diag) + elif ofmt == "abacus": + create_disturbs_abacus_dev(fin, nfile, dmax, etmax, + ofmt, dstyle, write_d, diag) \ No newline at end of file diff --git a/dpgen/data/tools/diamond.py b/dpgen/data/tools/diamond.py index 83f06b8b7..4674ef737 100644 --- a/dpgen/data/tools/diamond.py +++ b/dpgen/data/tools/diamond.py @@ -24,4 +24,3 @@ def poscar_unit (latt) : ret += "%.16f %.16f %.16f\n" % (0.12500000000000, 0.12500000000000, 0.12500000000000) ret += "%.16f %.16f %.16f\n" % (0.87500000000000, 0.87500000000000, 0.87500000000000) return ret - diff --git a/dpgen/data/tools/fcc.py b/dpgen/data/tools/fcc.py index be26bff59..ca4640bc1 100644 --- a/dpgen/data/tools/fcc.py +++ b/dpgen/data/tools/fcc.py @@ -22,4 +22,3 @@ def poscar_unit (latt) : ret += "%.16f %.16f %.16f\n" % (0.5, 0.0, 0.5) ret += "%.16f %.16f %.16f\n" % (0.0, 0.5, 0.5) return ret - diff --git a/dpgen/data/tools/hcp.py b/dpgen/data/tools/hcp.py index ed31a260f..b2a47ace9 100644 --- a/dpgen/data/tools/hcp.py +++ b/dpgen/data/tools/hcp.py @@ -23,4 +23,3 @@ def poscar_unit (latt) : ret += "%.16f %.16f %.16f\n" % (0, 0, 0) ret += "%.16f %.16f %.16f\n" % (1./3, 1./3, 1./2) return ret - diff --git a/dpgen/data/tools/sc.py b/dpgen/data/tools/sc.py index 3b1c4abe5..3e1c33d54 100644 --- a/dpgen/data/tools/sc.py +++ b/dpgen/data/tools/sc.py @@ -19,4 +19,3 @@ def poscar_unit (latt) : ret += "Direct\n" ret += "%.16f %.16f %.16f\n" % (0.0, 0.0, 0.0) return ret - diff --git a/dpgen/generator/lib/abacus_scf.py b/dpgen/generator/lib/abacus_scf.py index 8e68f91aa..fde813487 100644 --- a/dpgen/generator/lib/abacus_scf.py +++ b/dpgen/generator/lib/abacus_scf.py @@ -1,4 +1,7 @@ import numpy as np +from dpdata.abacus.scf import get_cell, get_coords +from dpgen.auto_test.lib.vasp import reciprocal_box +import os bohr2ang = 0.52917721067 def make_abacus_scf_kpt(fp_params): # Make KPT file for abacus pw scf calculation. @@ -80,22 +83,24 @@ def make_abacus_scf_input(fp_params): ret += "model_file %s\n" % fp_params["model_file"] return ret -def make_abacus_scf_stru(sys_data, fp_pp_files, fp_params): +def make_abacus_scf_stru(sys_data, fp_pp_files, fp_params = None): atom_names = sys_data['atom_names'] atom_numbs = sys_data['atom_numbs'] assert(len(atom_names) == len(fp_pp_files)), "the number of pp_files must be equal to the number of atom types. " assert(len(atom_names) == len(atom_numbs)), "Please check the name of atoms. " - cell = sys_data["cells"][0].reshape([3, 3]) - coord = sys_data['coords'][0] + cell = sys_data["cells"].reshape([3, 3]) + coord = sys_data['coords'].reshape([sum(atom_numbs), 3]) #volume = np.linalg.det(cell) #lattice_const = np.power(volume, 1/3) ret = "ATOMIC_SPECIES\n" for iatom in range(len(atom_names)): - ret += atom_names[iatom] + " 1.00 " + fp_pp_files[iatom] + "\n" - ret += "\n" + if 'atom_masses' not in sys_data: + ret += atom_names[iatom] + " 1.00 " + fp_pp_files[iatom] + "\n" + else: + ret += atom_names[iatom] + " %.3f "%sys_data['atom_masses'][iatom] + fp_pp_files[iatom] + "\n" - if "lattice_constant" in fp_params: + if fp_params is not None and "lattice_constant" in fp_params: ret += "\nLATTICE_CONSTANT\n" ret += str(fp_params["lattice_constant"]) + "\n\n" # in Bohr, in this way coord and cell are in Angstrom else: @@ -111,29 +116,149 @@ def make_abacus_scf_stru(sys_data, fp_pp_files, fp_params): ret += "ATOMIC_POSITIONS\n" ret += "Cartesian # Cartesian(Unit is LATTICE_CONSTANT)\n" - ret += "\n" + #ret += "\n" natom_tot = 0 for iele in range(len(atom_names)): ret += atom_names[iele] + "\n" ret += "0.0\n" ret += str(atom_numbs[iele]) + "\n" for iatom in range(atom_numbs[iele]): - ret += "%.12f %.12f %.12f %d %d %d\n" % (coord[natom_tot, 0], coord[natom_tot, 1], coord[natom_tot, 2], 0, 0, 0) + ret += "%.12f %.12f %.12f %d %d %d\n" % (coord[natom_tot, 0], coord[natom_tot, 1], coord[natom_tot, 2], 1, 1, 1) natom_tot += 1 assert(natom_tot == sum(atom_numbs)) - if "basis_type" in fp_params and fp_params["basis_type"]=="lcao": + if fp_params is not None and "basis_type" in fp_params and fp_params["basis_type"]=="lcao": ret +="\nNUMERICAL_ORBITAL\n" assert(len(fp_params["orb_files"])==len(atom_names)) for iatom in range(len(atom_names)): ret += fp_params["orb_files"][iatom] +"\n" - if "deepks_scf" in fp_params and fp_params["out_descriptor"]==1: + if fp_params is not None and "deepks_scf" in fp_params and fp_params["out_descriptor"]==1: ret +="\nNUMERICAL_DESCRIPTOR\n" ret +=fp_params["proj_file"][0]+"\n" return ret +def get_abacus_input_parameters(INPUT): + with open(INPUT) as fp: + inlines = fp.read().split("\n") + input_parameters = {} + for line in inlines: + if line.split() == [] or len(line.split()) < 2 : + continue + parameter_name = line.split()[0] + parameter_value = line.split()[1] + input_parameters[parameter_name] = parameter_value + return input_parameters + +def get_mass_from_STRU(geometry_inlines, inlines, atom_names): + nele = None + for line in inlines: + if line.split() == []: + continue + if "ntype" in line and "ntype" == line.split()[0]: + nele = int(line.split()[1]) + assert(nele is not None) + mass_list = [0 for i in atom_names] + pp_file_list = [i for i in atom_names] + for iline, line in enumerate(geometry_inlines): + if line.split() == []: + continue + if "ATOMIC_SPECIES" == line.split()[0]: + for iele1 in range(1, 1+nele): + for iele2 in range(nele): + if geometry_inlines[iline+iele1].split()[0] == atom_names[iele2]: + mass_list[iele2] = float(geometry_inlines[iline+iele1].split()[1]) + pp_file_list[iele2] = geometry_inlines[iline+iele1].split()[2] + for iele in range(len(mass_list)): + assert(mass_list[iele] > 0) + return mass_list, pp_file_list + +def get_natoms_from_stru(geometry_inlines): + key_words_list = ["ATOMIC_SPECIES", "NUMERICAL_ORBITAL", "LATTICE_CONSTANT", "LATTICE_VECTORS", "ATOMIC_POSITIONS"] + keyword_sequence = [] + keyword_line_index = [] + atom_names = [] + atom_numbs = [] + for iline, line in enumerate(geometry_inlines): + if line.split() == []: + continue + have_key_word = False + for keyword in key_words_list: + if keyword in line and keyword == line.split()[0]: + keyword_sequence.append(keyword) + keyword_line_index.append(iline) + assert(len(keyword_line_index) == len(keyword_sequence)) + assert(len(keyword_sequence) > 0) + keyword_line_index.append(len(geometry_inlines)) + for idx, keyword in enumerate(keyword_sequence): + if keyword == "ATOMIC_POSITIONS": + iline = keyword_line_index[idx]+2 + while iline < keyword_line_index[idx+1]-1: + atom_names.append(geometry_inlines[iline].split()[0]) + atom_numbs.append(int(geometry_inlines[iline+2].split()[0])) + iline += 3+atom_numbs[-1] + return atom_names, atom_numbs +def get_abacus_STRU(STRU, INPUT = None, n_ele = None): + # read in geometry from STRU file. n_ele is the number of elements. + # Either n_ele or INPUT should be provided. + with open(STRU, 'r') as fp: + geometry_inlines = fp.read().split('\n') + for iline, line in enumerate(geometry_inlines): + if line.split() == []: + del geometry_inlines[iline] + geometry_inlines.append("") + celldm, cell = get_cell(geometry_inlines) + if n_ele is None and INPUT is not None: + assert(os.path.isfile(INPUT)), "file %s should exists" % INPUT + with open(INPUT, 'r') as fp: + inlines = fp.read().split('\n') + atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) + elif n_ele is not None and INPUT is None: + assert(n_ele > 0) + inlines = ["ntype %d" %n_ele] + atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) + else: + atom_names, atom_numbs = get_natoms_from_stru(geometry_inlines) + inlines = ["ntype %d" %len(atom_numbs)] + atom_names, natoms, types, coords = get_coords(celldm, cell, geometry_inlines, inlines) + masses, pp_files = get_mass_from_STRU(geometry_inlines, inlines, atom_names) + data = {} + data['atom_names'] = atom_names + data['atom_numbs'] = natoms + data['atom_types'] = types + data['cells'] = cell + data['coords'] = coords + data['atom_masses'] = masses # Notice that this key is not defined in dpdata system. + data['pp_files'] = pp_files + return data + +def make_supercell_abacus(from_struct, super_cell): + if "types" in from_struct: + from_struct["types"] = from_struct["types"] * super_cell[0] * super_cell[1] * super_cell[2] + for ix in range(super_cell[0]): + for iy in range(super_cell[1]): + for iz in range(super_cell[2]): + if ix == 0 and iy == 0 and iz == 0: + continue + for ia in range(sum(from_struct["atom_numbs"])): + coord = from_struct['coords'][ia] + from_struct['cells'][0]*ix + from_struct['cells'][1]*iy + from_struct['cells'][2]*iz + from_struct['coords'] = np.vstack([from_struct['coords'], coord]) + from_struct["atom_numbs"] = [i * super_cell[0] * super_cell[1] * super_cell[2] for i in from_struct["atom_numbs"]] + from_struct['cells'][0] *= super_cell[0] + from_struct['cells'][1] *= super_cell[1] + from_struct['cells'][2] *= super_cell[2] + return from_struct + +def make_kspacing_kpoints_stru(stru, kspacing) : + # adapted from dpgen.autotest.lib.vasp.make_kspacing_kpoints + if type(kspacing) is not list: + kspacing = [kspacing, kspacing, kspacing] + box = stru['cells'] + rbox = reciprocal_box(box) + kpoints = [max(1,(np.ceil(2 * np.pi * np.linalg.norm(ii) / ks).astype(int))) for ii,ks in zip(rbox,kspacing)] + kpoints += [0, 0, 0] + return kpoints if __name__ == "__main__": fp_params = {"k_points": [1, 1, 1, 0, 0, 0]} diff --git a/dpgen/generator/lib/pwscf.py b/dpgen/generator/lib/pwscf.py index 8df25698d..94a454698 100644 --- a/dpgen/generator/lib/pwscf.py +++ b/dpgen/generator/lib/pwscf.py @@ -127,11 +127,14 @@ def _make_pwscf_04_kpoints(sys_data, kspacing): kpoints = [(np.ceil(2 * np.pi * np.linalg.norm(ii) / kspacing).astype(int)) for ii in rcell] ret = "" - ret += "K_POINTS { automatic }\n" - for ii in range(3) : - ret += "%d " % kpoints[ii] - for ii in range(3) : - ret += "%d " % _kshift(kpoints[ii]) + if kpoints == [1,1,1]: + ret += "K_POINTS gamma" + else: + ret += "K_POINTS { automatic }\n" + for ii in range(3) : + ret += "%d " % kpoints[ii] + for ii in range(3) : + ret += "%d " % _kshift(kpoints[ii]) ret += "\n" return ret diff --git a/dpgen/generator/run.py b/dpgen/generator/run.py index 1c4733037..67cca9e82 100644 --- a/dpgen/generator/run.py +++ b/dpgen/generator/run.py @@ -389,9 +389,13 @@ def make_train (iter_index, if jinput['model']['descriptor']['type'] == 'hybrid': for desc in jinput['model']['descriptor']['list']: desc['seed'] = random.randrange(sys.maxsize) % (2**32) + elif jinput['model']['descriptor']['type'] == 'loc_frame': + pass else: jinput['model']['descriptor']['seed'] = random.randrange(sys.maxsize) % (2**32) jinput['model']['fitting_net']['seed'] = random.randrange(sys.maxsize) % (2**32) + if 'type_embedding' in jinput['model']: + jinput['model']['type_embedding']['seed'] = random.randrange(sys.maxsize) % (2**32) jinput['training']['seed'] = random.randrange(sys.maxsize) % (2**32) else: raise RuntimeError("DP-GEN currently only supports for DeePMD-kit 1.x or 2.x version!" ) diff --git a/dpgen/simplify/simplify.py b/dpgen/simplify/simplify.py index 768d64835..8deb5a918 100644 --- a/dpgen/simplify/simplify.py +++ b/dpgen/simplify/simplify.py @@ -22,11 +22,13 @@ from dpgen import dlog from dpgen import SHORT_CMD from dpgen.util import sepline -from dpgen.dispatcher.Dispatcher import Dispatcher, make_dispatcher +from distutils.version import LooseVersion +from dpgen.dispatcher.Dispatcher import Dispatcher, _split_tasks, make_dispatcher, make_submission from dpgen.generator.run import make_train, run_train, post_train, run_fp, post_fp, fp_name, model_devi_name, train_name, train_task_fmt, sys_link_fp_vasp_pp, make_fp_vasp_incar, make_fp_vasp_kp, make_fp_vasp_cp_cvasp, data_system_fmt, model_devi_task_fmt, fp_task_fmt # TODO: maybe the following functions can be moved to dpgen.util from dpgen.generator.lib.utils import log_iter, make_iter_name, create_path, record_iter from dpgen.generator.lib.gaussian import make_gaussian_input +from dpgen.remote.decide_machine import convert_mdata picked_data_name = "data.picked" @@ -244,7 +246,7 @@ def run_model_devi(iter_index, jdata, mdata): commands = [] detail_file_names = [] for ii, mm in enumerate(task_model_list): - detail_file_name = "{prefix}.{ii}".format( + detail_file_name = "{prefix}-{ii}".format( prefix=detail_file_name_prefix, ii=ii, ) @@ -267,8 +269,12 @@ def run_model_devi(iter_index, jdata, mdata): forward_files = [rest_data_name] backward_files = sum([[pf+".e.out", pf+".f.out", pf+".v.out"] for pf in detail_file_names], []) - dispatcher = make_dispatcher(mdata['model_devi_machine'], mdata['model_devi_resources'], work_path, run_tasks, model_devi_group_size) - dispatcher.run_jobs(mdata['model_devi_resources'], + api_version = mdata.get('api_version', '0.9') + if LooseVersion(api_version) < LooseVersion('1.0'): + warnings.warn(f"the dpdispatcher will be updated to new version." + f"And the interface may be changed. Please check the documents for more details") + dispatcher = make_dispatcher(mdata['model_devi_machine'], mdata['model_devi_resources'], work_path, run_tasks, model_devi_group_size) + dispatcher.run_jobs(mdata['model_devi_resources'], commands, work_path, run_tasks, @@ -276,8 +282,23 @@ def run_model_devi(iter_index, jdata, mdata): model_names, forward_files, backward_files, - outlog='model_devi.log', - errlog='model_devi.log') + outlog = 'model_devi.log', + errlog = 'model_devi.log') + + elif LooseVersion(api_version) >= LooseVersion('1.0'): + submission = make_submission( + mdata['model_devi_machine'], + mdata['model_devi_resources'], + commands=commands, + work_path=work_path, + run_tasks=run_tasks, + group_size=model_devi_group_size, + forward_common_files=model_names, + forward_files=forward_files, + backward_files=backward_files, + outlog = 'model_devi.log', + errlog = 'model_devi.log') + submission.run_submission() def post_model_devi(iter_index, jdata, mdata): @@ -308,13 +329,13 @@ def post_model_devi(iter_index, jdata, mdata): sys_name = os.path.basename(task).split('.')[1] all_names.add(sys_name) # e.out - details_e = glob.glob(os.path.join(task, "{}.*.e.out".format(detail_file_name_prefix))) + details_e = glob.glob(os.path.join(task, "{}-*.e.out".format(detail_file_name_prefix))) e_all = np.array([np.loadtxt(detail_e, ndmin=2)[:, 1] for detail_e in details_e]) e_std = np.std(e_all, axis=0) n_frame = e_std.size # f.out - details_f = glob.glob(os.path.join(task, "{}.*.f.out".format(detail_file_name_prefix))) + details_f = glob.glob(os.path.join(task, "{}-*.f.out".format(detail_file_name_prefix))) f_all = np.array([np.loadtxt(detail_f, ndmin=2)[:, 3:6].reshape((n_frame, -1, 3)) for detail_f in details_f]) # (n_model, n_frame, n_atom, 3) f_std = np.std(f_all, axis=0) diff --git a/examples/init/abacus/CuW.json b/examples/init/abacus/CuW.json new file mode 100644 index 000000000..bfa0b8dba --- /dev/null +++ b/examples/init/abacus/CuW.json @@ -0,0 +1,37 @@ +{ + "init_fp_style": "ABACUS", + "stages": [1, 2, 3, 4], + "cell_type": "fcc", + "latt": 3.76, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Cu", "W" + ], + "atom_masses": [63.55, 183.8], + "potcars": [ + "Cu_ONCV_PBE-1.0.upf", + "W_ONCV_PBE-1.0.upf" + ], + "relax_incar": "INPUT", + "relax_kpt": "KPT", + "md_kpt": "KPT", + "md_incar": "INPUT.md", + "scale": [ + 0.99 + ], + "skip_relax": true, + "pert_numb": 2, + "md_nstep": 2, + "pert_box": 0.01, + "pert_atom": 0.01, + "coll_ndata": 12, + "type_map": [ + "Cu", + "W" + ], + "_comment": "that's all" +} diff --git a/examples/init/abacus/INPUT b/examples/init/abacus/INPUT new file mode 100644 index 000000000..e6fce1bcf --- /dev/null +++ b/examples/init/abacus/INPUT @@ -0,0 +1,19 @@ +INPUT_PARAMETERS + +calculation relax +atom_file STRU +kpoint_file KPT +pseudo_dir ./ +ntype 2 +symmetry 1 +ecutwfc 90 + +npool 4 +charge_extrap second-order +mixing_type pulay +mixing_beta 0.4 +dr2 1e-6 +nstep 3 +force_thr_ev 0.02 +move_method cg +out_stru 0 diff --git a/examples/init/abacus/INPUT.md b/examples/init/abacus/INPUT.md new file mode 100644 index 000000000..f9d59da2b --- /dev/null +++ b/examples/init/abacus/INPUT.md @@ -0,0 +1,19 @@ +INPUT_PARAMETERS + +calculation md +atom_file STRU +kpoint_file KPT +pseudo_dir ./ +ntype 2 +symmetry 1 +ecutwfc 90 + +npool 4 +charge_extrap second-order +mixing_type pulay +mixing_beta 0.4 +dr2 1e-6 +nstep 1 +force_thr_ev 0.02 +move_method cg +out_stru 0 diff --git a/tests/data/CuW.json b/tests/data/CuW.json new file mode 100644 index 000000000..4d289710e --- /dev/null +++ b/tests/data/CuW.json @@ -0,0 +1,37 @@ +{ + "init_fp_style": "ABACUS", + "stages": [1, 2, 3, 4], + "cell_type": "fcc", + "latt": 3.76, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Cu", "W" + ], + "atom_masses": [63.55, 183.8], + "potcars": [ + "abacus.in/Cu_ONCV_PBE-1.0.upf", + "abacus.in/W_ONCV_PBE-1.0.upf" + ], + "relax_incar": "abacus.in/INPUT", + "relax_kpt": "abacus.in/KPT", + "md_kpt": "abacus.in/KPT", + "md_incar": "abacus.in/INPUT.md", + "scale": [ + 0.99 + ], + "skip_relax": true, + "pert_numb": 2, + "md_nstep": 2, + "pert_box": 0.01, + "pert_atom": 0.01, + "coll_ndata": 12, + "type_map": [ + "Cu", + "W" + ], + "_comment": "that's all" +} diff --git a/tests/data/abacus.in/Cu_ONCV_PBE-1.0.upf b/tests/data/abacus.in/Cu_ONCV_PBE-1.0.upf new file mode 100644 index 000000000..206d35302 --- /dev/null +++ b/tests/data/abacus.in/Cu_ONCV_PBE-1.0.upf @@ -0,0 +1,1555 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + Cu 29.00 3 4 4 upf +# +# n l f energy (Ha) + 1 0 2.00 + 2 0 2.00 + 2 1 6.00 + 3 0 2.00 + 3 1 6.00 + 4 0 2.00 + 3 2 9.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 2 +# +# l, rc, ep, ncon, nbas, qcut + 0 1.91598 -4.40982 5 8 6.64634 + 1 1.87081 -2.84099 5 8 7.69831 + 2 1.89326 -0.34980 5 8 8.82467 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 1.68037 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 4.19623 + 1 2 2.79795 + 2 2 0.83231 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 0.0800 0.0900 0.1000 0.1100 0.1200 0.1300 0.1400 0.1500 + 0.1600 0.1700 0.1800 0.1900 0.2000 0.2100 0.2200 0.2300 + 0.2400 0.2500 0.2600 0.2700 0.2800 0.2900 0.3000 0.3100 + 0.3200 0.3300 0.3400 0.3500 0.3600 0.3700 0.3800 0.3900 + 0.4000 0.4100 0.4200 0.4300 0.4400 0.4500 0.4600 0.4700 + 0.4800 0.4900 0.5000 0.5100 0.5200 0.5300 0.5400 0.5500 + 0.5600 0.5700 0.5800 0.5900 0.6000 0.6100 0.6200 0.6300 + 0.6400 0.6500 0.6600 0.6700 0.6800 0.6900 0.7000 0.7100 + 0.7200 0.7300 0.7400 0.7500 0.7600 0.7700 0.7800 0.7900 + 0.8000 0.8100 0.8200 0.8300 0.8400 0.8500 0.8600 0.8700 + 0.8800 0.8900 0.9000 0.9100 0.9200 0.9300 0.9400 0.9500 + 0.9600 0.9700 0.9800 0.9900 1.0000 1.0100 1.0200 1.0300 + 1.0400 1.0500 1.0600 1.0700 1.0800 1.0900 1.1000 1.1100 + 1.1200 1.1300 1.1400 1.1500 1.1600 1.1700 1.1800 1.1900 + 1.2000 1.2100 1.2200 1.2300 1.2400 1.2500 1.2600 1.2700 + 1.2800 1.2900 1.3000 1.3100 1.3200 1.3300 1.3400 1.3500 + 1.3600 1.3700 1.3800 1.3900 1.4000 1.4100 1.4200 1.4300 + 1.4400 1.4500 1.4600 1.4700 1.4800 1.4900 1.5000 1.5100 + 1.5200 1.5300 1.5400 1.5500 1.5600 1.5700 1.5800 1.5900 + 1.6000 1.6100 1.6200 1.6300 1.6400 1.6500 1.6600 1.6700 + 1.6800 1.6900 1.7000 1.7100 1.7200 1.7300 1.7400 1.7500 + 1.7600 1.7700 1.7800 1.7900 1.8000 1.8100 1.8200 1.8300 + 1.8400 1.8500 1.8600 1.8700 1.8800 1.8900 1.9000 1.9100 + 1.9200 1.9300 1.9400 1.9500 1.9600 1.9700 1.9800 1.9900 + 2.0000 2.0100 2.0200 2.0300 2.0400 2.0500 2.0600 2.0700 + 2.0800 2.0900 2.1000 2.1100 2.1200 2.1300 2.1400 2.1500 + 2.1600 2.1700 2.1800 2.1900 2.2000 2.2100 2.2200 2.2300 + 2.2400 2.2500 2.2600 2.2700 2.2800 2.2900 2.3000 2.3100 + 2.3200 2.3300 2.3400 2.3500 2.3600 2.3700 2.3800 2.3900 + 2.4000 2.4100 2.4200 2.4300 2.4400 2.4500 2.4600 2.4700 + 2.4800 2.4900 2.5000 2.5100 2.5200 2.5300 2.5400 2.5500 + 2.5600 2.5700 2.5800 2.5900 2.6000 2.6100 2.6200 2.6300 + 2.6400 2.6500 2.6600 2.6700 2.6800 2.6900 2.7000 2.7100 + 2.7200 2.7300 2.7400 2.7500 2.7600 2.7700 2.7800 2.7900 + 2.8000 2.8100 2.8200 2.8300 2.8400 2.8500 2.8600 2.8700 + 2.8800 2.8900 2.9000 2.9100 2.9200 2.9300 2.9400 2.9500 + 2.9600 2.9700 2.9800 2.9900 3.0000 3.0100 3.0200 3.0300 + 3.0400 3.0500 3.0600 3.0700 3.0800 3.0900 3.1000 3.1100 + 3.1200 3.1300 3.1400 3.1500 3.1600 3.1700 3.1800 3.1900 + 3.2000 3.2100 3.2200 3.2300 3.2400 3.2500 3.2600 3.2700 + 3.2800 3.2900 3.3000 3.3100 3.3200 3.3300 3.3400 3.3500 + 3.3600 3.3700 3.3800 3.3900 3.4000 3.4100 3.4200 3.4300 + 3.4400 3.4500 3.4600 3.4700 3.4800 3.4900 3.5000 3.5100 + 3.5200 3.5300 3.5400 3.5500 3.5600 3.5700 3.5800 3.5900 + 3.6000 3.6100 3.6200 3.6300 3.6400 3.6500 3.6600 3.6700 + 3.6800 3.6900 3.7000 3.7100 3.7200 3.7300 3.7400 3.7500 + 3.7600 3.7700 3.7800 3.7900 3.8000 3.8100 3.8200 3.8300 + 3.8400 3.8500 3.8600 3.8700 3.8800 3.8900 3.9000 3.9100 + 3.9200 3.9300 3.9400 3.9500 3.9600 3.9700 3.9800 3.9900 + 4.0000 4.0100 4.0200 4.0300 4.0400 4.0500 4.0600 4.0700 + 4.0800 4.0900 4.1000 4.1100 4.1200 4.1300 4.1400 4.1500 + 4.1600 4.1700 4.1800 4.1900 4.2000 4.2100 4.2200 4.2300 + 4.2400 4.2500 4.2600 4.2700 4.2800 4.2900 4.3000 4.3100 + 4.3200 4.3300 4.3400 4.3500 4.3600 4.3700 4.3800 4.3900 + 4.4000 4.4100 4.4200 4.4300 4.4400 4.4500 4.4600 4.4700 + 4.4800 4.4900 4.5000 4.5100 4.5200 4.5300 4.5400 4.5500 + 4.5600 4.5700 4.5800 4.5900 4.6000 4.6100 4.6200 4.6300 + 4.6400 4.6500 4.6600 4.6700 4.6800 4.6900 4.7000 4.7100 + 4.7200 4.7300 4.7400 4.7500 4.7600 4.7700 4.7800 4.7900 + 4.8000 4.8100 4.8200 4.8300 4.8400 4.8500 4.8600 4.8700 + 4.8800 4.8900 4.9000 4.9100 4.9200 4.9300 4.9400 4.9500 + 4.9600 4.9700 4.9800 4.9900 5.0000 5.0100 5.0200 5.0300 + 5.0400 5.0500 5.0600 5.0700 5.0800 5.0900 5.1000 5.1100 + 5.1200 5.1300 5.1400 5.1500 5.1600 5.1700 5.1800 5.1900 + 5.2000 5.2100 5.2200 5.2300 5.2400 5.2500 5.2600 5.2700 + 5.2800 5.2900 5.3000 5.3100 5.3200 5.3300 5.3400 5.3500 + 5.3600 5.3700 5.3800 5.3900 5.4000 5.4100 5.4200 5.4300 + 5.4400 5.4500 5.4600 5.4700 5.4800 5.4900 5.5000 5.5100 + 5.5200 5.5300 5.5400 5.5500 5.5600 5.5700 5.5800 5.5900 + 5.6000 5.6100 5.6200 5.6300 5.6400 5.6500 5.6600 5.6700 + 5.6800 5.6900 5.7000 5.7100 5.7200 5.7300 5.7400 5.7500 + 5.7600 5.7700 5.7800 5.7900 5.8000 5.8100 5.8200 5.8300 + 5.8400 5.8500 5.8600 5.8700 5.8800 5.8900 5.9000 5.9100 + 5.9200 5.9300 5.9400 5.9500 5.9600 5.9700 5.9800 5.9900 + 6.0000 6.0100 + + + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 0.0100 + 0.0100 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3.8696715386E-02 3.8250137031E-02 3.7808513838E-02 3.7371792434E-02 + 3.6939915270E-02 3.6512723217E-02 3.6090276509E-02 3.5672529401E-02 + 3.5259434800E-02 3.4850944261E-02 3.4447007976E-02 3.4047574768E-02 + 3.3652492114E-02 3.3261813874E-02 3.2875500714E-02 3.2493508792E-02 + 3.2115793029E-02 3.1742307110E-02 + + diff --git a/tests/data/abacus.in/INPUT b/tests/data/abacus.in/INPUT new file mode 100644 index 000000000..e6fce1bcf --- /dev/null +++ b/tests/data/abacus.in/INPUT @@ -0,0 +1,19 @@ +INPUT_PARAMETERS + +calculation relax +atom_file STRU +kpoint_file KPT +pseudo_dir ./ +ntype 2 +symmetry 1 +ecutwfc 90 + +npool 4 +charge_extrap second-order +mixing_type pulay +mixing_beta 0.4 +dr2 1e-6 +nstep 3 +force_thr_ev 0.02 +move_method cg +out_stru 0 diff --git a/tests/data/abacus.in/INPUT.md b/tests/data/abacus.in/INPUT.md new file mode 100644 index 000000000..f9d59da2b --- /dev/null +++ b/tests/data/abacus.in/INPUT.md @@ -0,0 +1,19 @@ +INPUT_PARAMETERS + +calculation md +atom_file STRU +kpoint_file KPT +pseudo_dir ./ +ntype 2 +symmetry 1 +ecutwfc 90 + +npool 4 +charge_extrap second-order +mixing_type pulay +mixing_beta 0.4 +dr2 1e-6 +nstep 1 +force_thr_ev 0.02 +move_method cg +out_stru 0 diff --git a/tests/data/abacus.in/KPT b/tests/data/abacus.in/KPT new file mode 100644 index 000000000..8f0b0b445 --- /dev/null +++ b/tests/data/abacus.in/KPT @@ -0,0 +1,4 @@ +K_POINTS +0 +Gamma +10 10 10 0 0 0 diff --git a/tests/data/abacus.in/W_ONCV_PBE-1.0.upf b/tests/data/abacus.in/W_ONCV_PBE-1.0.upf new file mode 100644 index 000000000..0052acf50 --- /dev/null +++ b/tests/data/abacus.in/W_ONCV_PBE-1.0.upf @@ -0,0 +1,1891 @@ + + + + This pseudopotential file has been produced using the code + ONCVPSP (Optimized Norm-Conservinng Vanderbilt PSeudopotential) + scalar-relativistic version 2.1.1, 03/26/2014 by D. R. Hamann + The code is available through a link at URL www.mat-simresearch.com. + Documentation with the package provides a full discription of the + input data below. + + + While it is not required under the terms of the GNU GPL, it is + suggested that you cite D. R. Hamann, Phys. Rev. B 88, 085117 (2013) + in any publication using these pseudopotentials. + + + Copyright 2015 The Regents of the University of California + + This work is licensed under the Creative Commons Attribution-ShareAlike + 4.0 International License. To view a copy of this license, visit + http://creativecommons.org/licenses/by-sa/4.0/ or send a letter to + Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. + + This pseudopotential is part of the Schlipf-Gygi norm-conserving + pseudopotential library. Its construction parameters were tuned to + reproduce materials of a training set with very high accuracy and + should be suitable as a general purpose pseudopotential to treat a + variety of different compounds. For details of the construction and + testing of the pseudopotential please refer to: + + [insert reference to paper here] + + We kindly ask that you include this reference in all publications + associated to this pseudopotential. + + + +# ATOM AND REFERENCE CONFIGURATION +# atsym z nc nv iexc psfile + W 74.00 9 5 4 upf +# +# n l f energy (Ha) + 1 0 2.00 + 2 0 2.00 + 2 1 6.00 + 3 0 2.00 + 3 1 6.00 + 3 2 10.00 + 4 0 2.00 + 4 1 6.00 + 4 2 10.00 + 4 3 14.00 + 5 0 2.00 + 5 1 6.00 + 6 0 2.00 + 5 2 4.00 +# +# PSEUDOPOTENTIAL AND OPTIMIZATION +# lmax + 3 +# +# l, rc, ep, ncon, nbas, qcut + 0 2.14508 -2.90589 5 8 7.75777 + 1 2.19687 -1.58765 5 8 7.39083 + 2 1.90387 -0.16465 5 8 8.12535 + 3 3.03164 -1.22033 5 8 7.15988 +# +# LOCAL POTENTIAL +# lloc, lpopt, rc(5), dvloc0 + 4 5 1.64995 0.00000 +# +# VANDERBILT-KLEINMAN-BYLANDER PROJECTORs +# l, nproj, debl + 0 2 2.69594 + 1 2 1.53763 + 2 2 1.03812 + 3 2 1.31707 +# +# MODEL CORE CHARGE +# icmod, fcfact + 0 0.00000 +# +# LOG DERIVATIVE ANALYSIS +# epsh1, epsh2, depsh + -5.00 3.00 0.02 +# +# OUTPUT GRID +# rlmax, drl + 6.00 0.01 +# +# TEST CONFIGURATIONS +# ncnf + 0 +# nvcnf +# n l f + + + + + + + + + 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700 + 0.0800 0.0900 0.1000 0.1100 0.1200 0.1300 0.1400 0.1500 + 0.1600 0.1700 0.1800 0.1900 0.2000 0.2100 0.2200 0.2300 + 0.2400 0.2500 0.2600 0.2700 0.2800 0.2900 0.3000 0.3100 + 0.3200 0.3300 0.3400 0.3500 0.3600 0.3700 0.3800 0.3900 + 0.4000 0.4100 0.4200 0.4300 0.4400 0.4500 0.4600 0.4700 + 0.4800 0.4900 0.5000 0.5100 0.5200 0.5300 0.5400 0.5500 + 0.5600 0.5700 0.5800 0.5900 0.6000 0.6100 0.6200 0.6300 + 0.6400 0.6500 0.6600 0.6700 0.6800 0.6900 0.7000 0.7100 + 0.7200 0.7300 0.7400 0.7500 0.7600 0.7700 0.7800 0.7900 + 0.8000 0.8100 0.8200 0.8300 0.8400 0.8500 0.8600 0.8700 + 0.8800 0.8900 0.9000 0.9100 0.9200 0.9300 0.9400 0.9500 + 0.9600 0.9700 0.9800 0.9900 1.0000 1.0100 1.0200 1.0300 + 1.0400 1.0500 1.0600 1.0700 1.0800 1.0900 1.1000 1.1100 + 1.1200 1.1300 1.1400 1.1500 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3.850590682409233079e+00 3.399700055381695840e+00 3.730032485145450494e+00 4.558979655559638466e+00 4.162695936402228014e+00 5.252297961232436307e+00 5.398442395905188818e+00 4.206437301393266104e+00 5.023908229323359897e+00 3.948874057084713840e+00 5.141254402247102284e+00 4.787753781670383901e+00 4.439366062742222674e+00 4.224171582619086429e+00 diff --git a/tests/data/abacus.out/energy.raw b/tests/data/abacus.out/energy.raw new file mode 100644 index 000000000..d6e8aa5d7 --- /dev/null +++ b/tests/data/abacus.out/energy.raw @@ -0,0 +1,9 @@ +-2.191299378191779965e+02 +-2.194405277004599952e+02 +-2.198624336150280101e+02 +-2.191326527145239993e+02 +-2.194421046524030032e+02 +-2.198623721410370138e+02 +-2.191187282189270036e+02 +-2.194341917153120107e+02 +-2.198612731451000002e+02 diff --git a/tests/data/abacus.out/force.raw b/tests/data/abacus.out/force.raw new file mode 100644 index 000000000..4144adc07 --- /dev/null +++ b/tests/data/abacus.out/force.raw @@ -0,0 +1,9 @@ +1.340516999999999959e+00 -2.319939999999999891e+00 -3.252981999999999818e+00 -4.366520999999999653e+00 5.253839999999999621e-01 -2.713240000000000096e-01 1.946277000000000035e+00 3.914839999999999876e+00 -1.002760000000000040e-01 9.686479999999999535e-01 -1.975710000000000077e+00 3.652965000000000018e+00 1.110799999999999982e-01 -1.445730000000000071e-01 -2.838299999999999851e-02 +1.004871000000000070e+00 -1.739881000000000011e+00 -2.441946999999999868e+00 -3.252618000000000009e+00 3.932160000000000100e-01 -2.014640000000000042e-01 1.449497000000000035e+00 2.920978999999999992e+00 -7.423100000000000531e-02 7.239849999999999897e-01 -1.478039000000000103e+00 2.737074999999999925e+00 7.426499999999999768e-02 -9.627499999999999947e-02 -1.943299999999999889e-02 +3.081909999999999927e-01 -5.357279999999999820e-01 -7.577249999999999819e-01 -9.752370000000000205e-01 1.223179999999999962e-01 -5.883499999999999841e-02 4.313279999999999892e-01 8.821980000000000377e-01 -2.097399999999999959e-02 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-1.585999999999999910e-02 -5.335600000000000065e-02 3.607400000000000051e-01 +3.706369999999999942e-01 -5.229000000000000314e-01 -7.455789999999999917e-01 -9.850360000000000227e-01 1.368810000000000027e-01 -6.710800000000000098e-02 4.571290000000000076e-01 8.672569999999999446e-01 -6.185999999999999832e-02 2.617059999999999942e-01 -4.714160000000000017e-01 8.086250000000000382e-01 -1.044360000000000011e-01 -9.821999999999999134e-03 6.592199999999999449e-02 diff --git a/tests/data/abacus.out/type.raw b/tests/data/abacus.out/type.raw new file mode 100644 index 000000000..0b21c0d0e --- /dev/null +++ b/tests/data/abacus.out/type.raw @@ -0,0 +1,5 @@ +0 +0 +0 +0 +1 diff --git a/tests/data/abacus.out/type_map.raw b/tests/data/abacus.out/type_map.raw new file mode 100644 index 000000000..35025b8b1 --- /dev/null +++ b/tests/data/abacus.out/type_map.raw @@ -0,0 +1,2 @@ +H +C diff --git a/tests/data/abacus.out/virial.raw b/tests/data/abacus.out/virial.raw new file mode 100644 index 000000000..81d860769 --- /dev/null +++ b/tests/data/abacus.out/virial.raw @@ -0,0 +1,9 @@ +5.795858174693855780e+00 3.443092965380536302e-02 1.929418518002443822e-02 3.443092965380536302e-02 5.716638835032358479e+00 -2.389685573149830794e-02 1.929418518002443822e-02 -2.389685573149830794e-02 5.617522216398079138e+00 +4.408988076950304702e+00 2.176542487386309843e-02 1.214803211126708540e-02 2.176542487386309843e-02 4.359248625442528002e+00 -1.506503678236161513e-02 1.214803211126708540e-02 -1.506503678236161513e-02 4.296671356642591810e+00 +1.386467678460361785e+00 -6.721258240496656147e-04 -3.665654374793160769e-04 -6.721258240496656147e-04 1.386947691887250755e+00 5.415536098234567707e-04 -3.665654374793160769e-04 5.415536098234567707e-04 1.389181332961759718e+00 +5.920273248601972682e+00 -6.039738868480488271e-02 -5.548276701405261552e-02 -6.039738868480488271e-02 5.605862281032128358e+00 1.215189545474988780e-01 -5.548276701405261552e-02 1.215189545474988780e-01 5.558883535614017823e+00 +4.490640109820734693e+00 -4.527006960785832923e-02 -4.134669356180990796e-02 -4.527006960785832923e-02 4.293001025437428453e+00 7.126623109612076346e-02 -4.134669356180990796e-02 7.126623109612076346e-02 4.248516980437247348e+00 +1.394114722102968162e+00 -1.766924844126081806e-02 -1.462129465140290206e-02 -1.766924844126081806e-02 1.399656251812032570e+00 -1.912491203874137902e-02 -1.462129465140290206e-02 -1.912491203874137902e-02 1.360744660235811310e+00 +5.844498499100296840e+00 -6.853191054575857519e-03 -1.324669162954480450e-01 -6.853191054575857519e-03 5.775330648915621978e+00 2.461468284624128700e-01 -1.324669162954480450e-01 2.461468284624128700e-01 5.611345206312754463e+00 +4.456000939126254501e+00 -1.359924298733263329e-02 -9.024508563996384847e-02 -1.359924298733263329e-02 4.394864279944473040e+00 1.488666274174575976e-01 -9.024508563996384847e-02 1.488666274174575976e-01 4.279539092748385620e+00 +1.432096287462409911e+00 -2.596479489866933624e-02 -1.308794539607722671e-02 -2.596479489866933624e-02 1.380061149718328606e+00 -2.498250948476371872e-02 -1.308794539607722671e-02 -2.498250948476371872e-02 1.354370036932820875e+00 diff --git a/tests/data/ch4.json b/tests/data/ch4.json new file mode 100644 index 000000000..7f3a74933 --- /dev/null +++ b/tests/data/ch4.json @@ -0,0 +1,26 @@ +{ + "init_fp_style": "ABACUS", + "stages": [1, 2, 3, 4], + "super_cell": [1, 1, 1], + "_comment": "if from_poscar = true, the cell_type and super_cell keys are actually useless", + "cell_type": "fcc", + "elements": ["H","C"], + "atom_masses": [1, 12], + "_comment": "if from_poscar = false, you have to set atom_masse.", + "out_dir": "./", + "from_poscar": true, + "from_poscar_path": "./STRU", + "potcars": ["./H_ONCV_PBE-1.0.upf", "./C_ONCV_PBE-1.0.upf"], + "relax_incar": "./INPUT", + "relax_kspacing": 10, + "md_incar" : "./INPUT.md", + "md_kspacing": 10, + "scale": [0.95], + "skip_relax": false, + "pert_numb": 2, + "md_nstep" : 3, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 10, + "_comment": "that's all" +} diff --git a/tests/data/context.py b/tests/data/context.py index 5d99787a5..b1d625352 100644 --- a/tests/data/context.py +++ b/tests/data/context.py @@ -3,6 +3,6 @@ from dpgen.data.gen import * param_file = 'al.json' - +abacus_param_file = 'ch4.json' def setUpModule(): os.chdir(os.path.abspath(os.path.dirname(__file__))) diff --git a/tests/data/context_bulk.py b/tests/data/context_bulk.py index 9696a6b9b..1a46b37bd 100644 --- a/tests/data/context_bulk.py +++ b/tests/data/context_bulk.py @@ -3,4 +3,4 @@ from dpgen.data.gen import * param_file = 'alloy.json' - +abacus_param_file = 'CuW.json' diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/INPUT new file mode 100644 index 000000000..c3181c397 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS + +calculation md +atom_file STRU +kpoint_file KPT +pseudo_dir ./ +ntype 2 +symmetry 1 +ecutwfc 90 + +npool 1 + +mixing_type pulay +mixing_beta 0.4 + +nstep 3 +force_thr_ev 0.02 +#move_method cg +out_stru 0 +stress 1 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/INPUT new file mode 100644 index 000000000..63bd0ed40 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/INPUT @@ -0,0 +1,263 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +atom_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir .// #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +renormwithmesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional none #exchange correlation functional +calculation md #test; scf; relax; nscf; ienvelope; istate; +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +nbands 0 #number of bands +nbands_sto 0 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +nche_sto 0 #number of orders for Chebyshev expansion in stochastic DFT +symmetry 0 #turn symmetry on or off +set_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system + +#Parameters (2.PW) +ecutwfc 90 ##energy cutoff for wave functions +diago_cg_maxiter 50 #max iteration number for cg +diago_cg_prec 1 #diago_cg_prec +ethr 0.01 #threshold for eigenvalues is cg electron iterations +dr2 1e-09 #charge density error +start_wfc atomic #start wave functions are from 'atomic' or 'file' +start_charge atomic #start charge is from 'atomic' or file +charge_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_charge 0 #>0 output charge density for selected electron steps +out_potential 0 #output realspace potential +out_wf 0 #output wave functions +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Relaxation) +ks_solver cg #cg; dav; lapack; genelpa; hpseps; scalapack_gvx +niter 40 ##number of electron iterations +force_set 0 #output the force_set or not +nstep 3 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.00077787 #force threshold, unit: Ry/Bohr +force_thr_ev 0.02 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +cg_threshold 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +bfgs_w1 0.01 #wolfe condition 1 for bfgs +bfgs_w2 0.5 #wolfe condition 2 for bfgs +trust_radius_max 0.8 #maximal trust radius, unit: Bohr +trust_radius_min 1e-05 #minimal trust radius, unit: Bohr +trust_radius_ini 0.5 #initial trust radius, unit: Bohr +stress 1 #calculate the stress or not +fixed_axes None #which axes are fixed +move_method cg #bfgs; sd; cg; cg_bfgs; +out_level m #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +out_descriptor 0 #>0 compute descriptor for deepks +lmax_descriptor 2 #>0 lmax used in descriptor for deepks + +#Parameters (4.LCAO) +basis_type pw #PW; LCAO in pw; LCAO +new_dm 1 #Type of density matrix; 0: old 1: new +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 0 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_hs 0 #output H and S matrix +out_hs2 0 #output H(R) and S(R) matrix +out_r 0 #output r(R) matrix +out_lowf 0 #ouput LCAO wave functions +bx 1 #division of an element grid in FFT grid along x +by 1 #division of an element grid in FFT grid along y +bz 1 #division of an element grid in FFT grid along z + +#Parameters (5.Smearing) +smearing fixed #type of smearing: gauss; fd; fixed; mp; mp2; mv +sigma 0.01 #energy range for smearing + +#Parameters (6.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (7.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) + +#Parameters (8.Technique) +gamma_only 0 #gamma only, only used in LCAO basis +diago_proc 8 #number of proc used to diago +npool 1 #number of pools for k points, pw only +mem_saver 0 #memory saver for many k points used +printe 100 #print band energy for selectively ionic steps + +#Parameters (9.SIAO) +selinv_npole 40 #number of selected poles +selinv_temp 2000 #temperature for Fermi-Dirac distribution +selinv_gap 0 #supposed gap in the calculation +selinv_deltae 2 #expected energy range +selinv_mu -1 #chosen mu as Fermi energy +selinv_threshold 0.001 #threshold for calculated electron number +selinv_niter 50 #max number of steps to update mu + +#Parameters (10.Molecular dynamics) +md_mdtype 1 #choose ensemble +md_potential FP #choose potential +md_dt 1 #time step +mnhc 4 #number of Nose-Hoover chains +md_qmass 1 #mass of thermostat +md_tfirst 0 #temperature first +md_tlast 0 #temperature last +md_dumpmdfred 1 #The period to dump MD information for monitoring and restarting MD +md_mdoutpath mdoutput #output path of md +md_rstmd 0 #whether restart +md_fixtemperature 1 #period to change temperature +md_ediff 0.0001 #parameter for constraining total energy change +md_ediffg 0.001 #parameter for constraining max force change +NVT_tau 0 #parameter for adjust effect of thermostat +NVT_control 1 #choose which thermostat used in NVT ensemble +rcut_lj 8.5 #cutoff radius of LJ potential +epsilon_lj 0.01032 #the value of epsilon for LJ potential +sigma_lj 3.405 #the value of sigma for LJ potential + +#Parameters (11.Efield) +efield 0 #add electric field +edir 1 #add electric field +emaxpos 0.5 #maximal position of efield [0,1) +eopreg 0.1 #where sawlike potential decrease +eamp 0.001 #amplitute of the efield, unit is a.u. +eamp_v 0.05144 #amplitute of the efield, unit is V/A + +#Parameters (12.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vxc_in_h 1 #calculate the xc potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.Other Methods) +mlwf_flag 0 #turn MLWF on or off +opt_epsilon2 0 #calculate the dielectic function +opt_nbands 0 #number of bands for optical calculation + +#Parameters (14.VdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (15.spectrum) +spectral_type None #the type of the calculated spectrum +spectral_method 0 #0: tddft(linear response) +kernel_type rpa #the kernel type: rpa, tdlda ... +eels_method 0 #0: hilbert_transform method; 1: standard method +absorption_method 0 #0: vasp's method 1: pwscf's method +system bulk #the calculate system +eta 0.05 #eta(Ry) +domega 0.01 #domega(Ry) +nomega 300 #nomega +ecut_chi 1 #the dimension of chi matrix +q_start 0.1 0.1 0.1 #the position of the first q point in direct coordinate +q_direction 1 0 0 #the q direction +nq 1 #the total number of qpoints for calculation +out_epsilon 1 #output epsilon or not +out_chi 0 #output chi or not +out_chi0 0 #output chi0 or not +fermi_level 0 #the change of the fermi_level(Ry) +coulomb_cutoff 0 # turn on the coulomb_cutoff or not +kmesh_interpolation 0 #calculting +qcar 0 0 0 #(unit: 2PI/lat0) +ocp 0 #change occupation or not +ocp_set none #set occupation +lcao_box 10 10 10 #the scale for searching the existence of the overlap + mulliken 0 # mulliken charge or not +intrasmear 0 #Eta +shift 0 #shift +metalcalc 0 #metal or not +eps_degauss 0.01 #degauss in calculating epsilon0 +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction + +#Parameters (17.exx) +exx_hybrid_type no #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (17.tddft) +tddft 0 #calculate tddft or not +td_dr2 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not + +#Parameters (18.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice std::vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_MD b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_MD new file mode 100644 index 000000000..ab99de324 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_MD @@ -0,0 +1,27 @@ +ATOMIC_SPECIES +H 1.008 H_ONCV_PBE-1.0.upf +C 12.01 C_ONCV_PBE-1.0.upf + +LATTICE_CONSTANT +1.88972612546 + +LATTICE_VECTORS +9.50000379042 0 0 #latvec1 +0 9.50000379042 0 #latvec2 +0 0 9.50000379042 #latvec3 + +ATOMIC_POSITIONS +Direct + +H #label +0 #magnetism +4 #number of atoms +0.540930980325 0.402075031383 0.353895874486 1 1 1 0 0 0 +0.385586980814 0.481402417362 0.437898545951 1 1 1 0 0 0 +0.556131217776 0.57347946396 0.442495090138 1 1 1 0 0 0 +0.530202220323 0.412321251956 0.546677526283 1 1 1 0 0 0 + +C #label +0 #magnetism +1 #number of atoms +0.503163091902 0.467364749224 0.445258850036 1 1 1 0 0 0 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_READIN_ADJUST.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 000000000..779ef9f3b --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.5 +_cell_length_b 9.5 +_cell_length_c 9.5 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.536573 0.40961 0.364448 +H 0.39961 0.479693 0.438774 +H 0.549844 0.56087 0.442817 +H 0.527061 0.418728 0.53486 +C 0.503135 0.467401 0.445266 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_1.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_1.cif new file mode 100644 index 000000000..e09204a1c --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_1.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.5 +_cell_length_b 9.5 +_cell_length_c 9.5 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.537248 0.408441 0.36281 +H 0.397411 0.479958 0.438637 +H 0.550825 0.562842 0.442767 +H 0.527549 0.417732 0.5367 +C 0.50314 0.467395 0.445265 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_2.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_2.cif new file mode 100644 index 000000000..99311ee37 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_2.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.5 +_cell_length_b 9.5 +_cell_length_c 9.5 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.538935 0.405522 0.358719 +H 0.391953 0.480618 0.438297 +H 0.553264 0.567743 0.442642 +H 0.528766 0.41525 0.541286 +C 0.503151 0.467381 0.445262 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_3.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_3.cif new file mode 100644 index 000000000..fde6898f6 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/md_pos_3.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.5 +_cell_length_b 9.5 +_cell_length_c 9.5 +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.540931 0.402075 0.353896 +H 0.385587 0.481402 0.437899 +H 0.556131 0.573479 0.442495 +H 0.530202 0.412321 0.546678 +C 0.503163 0.467365 0.445259 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/running_md.log b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/running_md.log new file mode 100644 index 000000000..34c025fe5 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/OUT.ABACUS/running_md.log @@ -0,0 +1,712 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 8 + Start Time is Fri Nov 12 18:15:13 2021 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 8 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = H + atom label for species 2 = C + lattice constant (Bohr) = 1.88973 + lattice constant (Angstrom) = 1 + + READING ATOM TYPE 1 + atom label = H + L=0, number of zeta = 1 + L=1, number of zeta = 1 + L=2, number of zeta = 1 + number of atom for this type = 4 + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = C + L=0, number of zeta = 1 + L=1, number of zeta = 1 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + TOTAL ATOM NUMBER = 5 + + CARTESIAN COORDINATES ( UNIT = 1.88973 Bohr ). + atom x y z mag vx vy vz + tauc_H1 5.09744437597 3.89129339419 3.4622612337 0 0 0 0 + tauc_H2 3.79629251291 4.55708480448 4.16835321433 0 0 0 0 + tauc_H3 5.2235234109 5.32826990334 4.20676661344 0 0 0 0 + tauc_H4 5.00707710352 3.97791420915 5.08117016892 0 0 0 0 + tauc_C1 4.77978417423 4.4403114594 4.23003031273 0 0 0 0 + + + Volume (Bohr^3) = 5785.86022047 + Volume (A^3) = 857.37500227 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +9.50000379042 +0 +0 + +0 +9.50000379042 +0 + +0 +0 +9.50000379042 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.105263115896 +0 +0 + +0 +0.105263115896 +0 + +0 +0 +0.105263115896 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is H_ONCV_PBE-1.0.upf + pseudopotential type = NC + functional Ex = PBE + functional Ec = + functional GCEx = + functional GCEc = + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is C_ONCV_PBE-1.0.upf + pseudopotential type = NC + functional Ex = PBE + functional Ec = + functional GCEx = + functional GCEc = + nonlocal core correction = 0 + valence electrons = 4 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + initial pseudo atomic orbital number = 0 + NLOCAL = 45 + + SETUP THE ELECTRONS NUMBER + electron number of element H = 1 + total electron number of element H = 4 + electron number of element C = 4 + total electron number of element C = 4 + occupied bands = 4 + NBANDS = 14 + DONE : SETUP UNITCELL Time : 0.086291129759 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0878850566805 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for wavefunc (unit:Ry) = 90 + [fft grid for wave functions] = 120, 120, 120 + [fft grid for charge/potential] = 120, 120, 120 + [fft grid division] = 1, 1, 1 + [big fft grid for charge/potential] = 120, 120, 120 + nbxx = 216000 + nrxx = 216000 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 667317 + number of sticks = 9249 + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + number of plane waves = 83599 + number of sticks = 2313 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 1155 83417 + 2 1157 83415 + 3 1157 83415 + 4 1156 83414 + 5 1156 83414 + 6 1156 83414 + 7 1156 83414 + 8 1156 83414 + --------------- sum ------------------- + 8 9249 667317 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(W) PW + 1 289 10449 + 2 289 10453 + 3 290 10452 + 4 287 10451 + 5 293 10449 + 6 290 10448 + 7 288 10448 + 8 287 10449 + --------------- sum ------------------- + 8 2313 83599 + + SETUP COORDINATES OF PLANE WAVES + number of total plane waves = 667317 + + SETUP COORDINATES OF PLANE WAVES + number of |g| = 2438 + max |g| = 32.553990643 + min |g| = 0 + DONE : INIT PLANEWAVE Time : 0.350971238862 (SEC) + + npwx = 10449 + + SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS + H non-local projectors: + projector 1 L=0 + projector 2 L=0 + C non-local projectors: + projector 1 L=0 + projector 2 L=0 + projector 3 L=1 + projector 4 L=1 + TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 + DONE : LOCAL POTENTIAL Time : 0.494807609997 (SEC) + + + Init Non-Local PseudoPotential table : + Init Non-Local-Pseudopotential done. + DONE : NON-LOCAL POTENTIAL Time : 0.501984705625 (SEC) + + start_pot = atomic + DONE : INIT POTENTIAL Time : 0.639263 (SEC) + + + Make real space PAO into reciprocal space. + max mesh points in Pseudopotential = 601 + dq(describe PAO in reciprocal space) = 0.01 + max q = 1143 + + number of pseudo atomic orbitals for H is 0 + + number of pseudo atomic orbitals for C is 0 + DONE : INIT BASIS Time : 0.917201 (SEC) + + ...............Nose-Hoover Chain parameter initialization............... + Temperature = 0 + Temperature2 = 0 + NHC frequency = 0.00120944 + NHC chain = 4 + Qmass = 1822.89 + ............................................................... + + PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + K-point CG iter num Time(Sec) + 1 9.642857 1.320000 + + Density error is 0.925917380140 + + PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + K-point CG iter num Time(Sec) + 1 2.357143 0.370000 + + Density error is 0.103089655783 + + PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + K-point CG iter num Time(Sec) + 1 4.500000 0.620000 + + Density error is 0.029305943975 + + PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + K-point CG iter num Time(Sec) + 1 3.928571 0.550000 + + Density error is 0.215036462399 + + PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + K-point CG iter num Time(Sec) + 1 3.285714 0.480000 + + Density error is 0.000079236362 + + PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + K-point CG iter num Time(Sec) + 1 6.857143 0.890000 + + Density error is 0.000065409462 + + PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + K-point CG iter num Time(Sec) + 1 3.071429 0.440000 + + Density error is 0.000015159186 + + PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + K-point CG iter num Time(Sec) + 1 5.214286 0.690000 + + Density error is 0.000000616832 + + PW ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + K-point CG iter num Time(Sec) + 1 4.357143 0.590000 + + Density error is 0.000000158907 + + PW ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + K-point CG iter num Time(Sec) + 1 5.857143 0.760000 + + Density error is 0.000000003032 + + PW ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + K-point CG iter num Time(Sec) + 1 6.500000 0.840000 + + Density error is 0.000000000145 + + charge density convergence is achieved + final etot is -219.129937819178 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +1.340517 -2.319940 -3.252982 + H2 -4.366521 +0.525384 -0.271324 + H3 +1.946277 +3.914840 -0.100276 + H4 +0.968648 -1.975710 +3.652965 + C1 +0.111080 -0.144573 -0.028383 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +10.830707 +0.064341 +0.036055 + +0.064341 +10.682670 -0.044656 + +0.036055 -0.044656 +10.497451 + +output Pressure for check! +Virtual Pressure is +21.340552 Kbar +Virial Term is +21.340552 Kbar +Kenetic Term is +0.000000 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 1 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -16.105748 (Rydberg) + NVT Temperature : +0.000000 (K) + NVT Kinetic energy : +0.000000 (Rydberg) + NVT Potential energy : -16.105748 (Rydberg) + maxForce : +0.007343 + maxStep : +0.039821 + MD_STEP SystemE Conserved DeltaE Temperature + +1 -8.052874 -8.052874 +0.000000 +172.203317 + + PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +53.714286 +6.150000 + + Density error is +0.003432405487 + + PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.214286 +0.340000 + + Density error is +0.000062275134 + + PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.000000 +0.530000 + + Density error is +0.000015792053 + + PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.142857 +0.450000 + + Density error is +0.000001338459 + + PW ALGORITHM --------------- ION=+2 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.642857 +0.610000 + + Density error is +0.000000192378 + + PW ALGORITHM --------------- ION=+2 ELEC=+6 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.142857 +0.460000 + + Density error is +0.000000025550 + + PW ALGORITHM --------------- ION=+2 ELEC=+7 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.714286 +0.640000 + + Density error is +0.000000014039 + + PW ALGORITHM --------------- ION=+2 ELEC=+8 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.142857 +0.330000 + + Density error is +0.000000005006 + + PW ALGORITHM --------------- ION=+2 ELEC=+9 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.428571 +0.370000 + + Density error is +0.000000001075 + + PW ALGORITHM --------------- ION=+2 ELEC=+10 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.571429 +0.630000 + + Density error is +0.000000000036 + + charge density convergence is achieved + final etot is -219.440527700460 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +1.004871 -1.739881 -2.441947 + H2 -3.252618 +0.393216 -0.201464 + H3 +1.449497 +2.920979 -0.074231 + H4 +0.723985 -1.478039 +2.737075 + C1 +0.074265 -0.096275 -0.019433 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +8.239066 +0.040673 +0.022701 + +0.040673 +8.146118 -0.028152 + +0.022701 -0.028152 +8.029180 + +output Pressure for check! +Virtual Pressure is +16.387160 Kbar +Virial Term is +16.276243 Kbar +Kenetic Term is +0.110917 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 2 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -16.108578 (Rydberg) + NVT Temperature : +526.047604 (K) + NVT Kinetic energy : +0.019991 (Rydberg) + NVT Potential energy : -16.128576 (Rydberg) + maxForce : +0.004075 + maxStep : +0.098572 + MD_STEP SystemE Conserved DeltaE Temperature + +2 -8.064288 -8.054289 +0.000000 +1063.334415 + + PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +54.857143 +6.240000 + + Density error is +0.019351753103 + + PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.214286 +0.340000 + + Density error is +0.000283196908 + + PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.071429 +0.550000 + + Density error is +0.000097414254 + + PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.785714 +0.410000 + + Density error is +0.000008367964 + + PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.857143 +0.540000 + + Density error is +0.000001252601 + + PW ALGORITHM --------------- ION=+3 ELEC=+6 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.642857 +0.510000 + + Density error is +0.000000066252 + + PW ALGORITHM --------------- ION=+3 ELEC=+7 -------------------------------- + K-point CG iter num Time(Sec) + +1 +5.071429 +0.670000 + + Density error is +0.000000013589 + + PW ALGORITHM --------------- ION=+3 ELEC=+8 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.571429 +0.610000 + + Density error is +0.000000024404 + + PW ALGORITHM --------------- ION=+3 ELEC=+9 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.320000 + + Density error is +0.000000010839 + + PW ALGORITHM --------------- ION=+3 ELEC=+10 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.071429 +0.340000 + + Density error is +0.000000002800 + + PW ALGORITHM --------------- ION=+3 ELEC=+11 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.000000 +0.550000 + + Density error is +0.000000000052 + + charge density convergence is achieved + final etot is -219.862433615028 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.308191 -0.535728 -0.757725 + H2 -0.975237 +0.122318 -0.058835 + H3 +0.431328 +0.882198 -0.020974 + H4 +0.218386 -0.449293 +0.842665 + C1 +0.017332 -0.019495 -0.005131 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +2.590889 -0.001256 -0.000685 + -0.001256 +2.591786 +0.001012 + -0.000685 +0.001012 +2.595960 + +output Pressure for check! +Virtual Pressure is +5.870656 Kbar +Virial Term is +5.185757 Kbar +Kenetic Term is +0.684900 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 3 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -16.111086 (Rydberg) + NVT Temperature : +1266.849197 (K) + NVT Kinetic energy : +0.048143 (Rydberg) + NVT Potential energy : -16.159585 (Rydberg) + maxForce : +0.000367 + maxStep : +0.114449 + MD_STEP SystemE Conserved DeltaE Temperature + +3 -8.079793 -8.055543 +0.000000 +1452.963348 + + + -------------------------------------------- + !FINAL_ETOT_IS -219.8624336150282090 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total +67.074 15 +4.47 +100.00 % + Run_pw plane_wave_line +67.04 1 +67.04 +99.95 % + PW_Basis gen_pw +0.26 1 +0.26 +0.39 % + Run_MD_PW md_cells_pw +66.70 1 +66.70 +99.45 % + ppcell_vl init_vloc +0.12 1 +0.12 +0.18 % + Potential init_pot +0.46 4 +0.11 +0.68 % + FFT FFT3D +26.79 8433 +0.00 +39.94 % + Charge atomic_rho +0.12 7 +0.02 +0.18 % + Potential v_of_rho +3.52 36 +0.10 +5.25 % + H_XC_pw v_xc +3.31 39 +0.08 +4.93 % + H_Hartree_pw v_hartree +0.42 36 +0.01 +0.63 % + wavefunc wfcinit +1.06 4 +0.26 +1.58 % + pp_cell_vnl getvnl +0.15 42 +0.00 +0.22 % + Hamilt_PW diagH_subspace +3.50 36 +0.10 +5.21 % + Hamilt_PW h_psi +27.80 3259 +0.01 +41.45 % + Hamilt_PW vloc +25.80 3259 +0.01 +38.46 % + Hamilt_PW vnl +1.91 3259 +0.00 +2.85 % + Hamilt_PW add_nonlocal_pp +0.90 3259 +0.00 +1.35 % + Run_MD_PW md_ions_pw +66.15 1 +66.15 +98.63 % + Electrons self_consistent +62.27 3 +20.76 +92.84 % + Electrons c_bands +29.33 32 +0.92 +43.73 % + Hamilt diagH_pw +29.20 32 +0.91 +43.54 % + Diago_CG diag +26.09 34 +0.77 +38.90 % + Charge sum_band +2.94 32 +0.09 +4.38 % + Charge rho_mpi +1.08 32 +0.03 +1.61 % + Charge mix_rho +0.97 32 +0.03 +1.45 % + Forces cal_force_nl +0.24 3 +0.08 +0.36 % + Stress_PW cal_stress +1.94 3 +0.65 +2.89 % + Stress_Func stress_ew +22.20 2 +11.10 +33.10 % + Force_Func stress_ew +22.20 2 +11.10 +33.10 % + Stress_Func stress_gga +0.13 3 +0.04 +0.19 % + Stress_Func stres_nl +1.63 3 +0.54 +2.43 % + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + +70.3196 + Charge_Pulay Rrho +13.1836 + Charge_Pulay dRrho +11.5356 + Charge_Pulay drho +11.5356 + Use_FFT porter +3.2959 + PW_Basis struc_fac +2.5457 + wavefunc evc +2.2321 + Charge rho +1.6479 + Charge rho_save +1.6479 + Charge rho_core +1.6479 + Potential vltot +1.6479 + Potential vr +1.6479 + Potential vr_eff +1.6479 + Potential vr_eff1 +1.6479 + Potential vnew +1.6479 + Charge_Pulay rho_save2 +1.6479 + ---------------------------------------------------------- + + Start Time : Fri Nov 12 18:15:13 2021 + Finish Time : Fri Nov 12 18:16:20 2021 + Total Time : 0 h 1 mins 7 secs diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/STRU b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/STRU new file mode 100644 index 000000000..9df80429c --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000000/STRU @@ -0,0 +1,25 @@ +ATOMIC_SPECIES +H 1.008 H_ONCV_PBE-1.0.upf +C 12.010 C_ONCV_PBE-1.0.upf + +LATTICE_CONSTANT +1.8897261254578281 + +LATTICE_VECTORS +9.500003790418825 0.0 0.0 +0.0 9.500003790418825 0.0 +0.0 0.0 9.500003790418825 + +ATOMIC_POSITIONS +Cartesian # Cartesian(Unit is LATTICE_CONSTANT) +H +0.0 +4 +5.097444375976 3.891293394194 3.462261233691 1 1 1 +3.796292512908 4.557084804487 4.168353214339 1 1 1 +5.223523410907 5.328269903334 4.206766613435 1 1 1 +5.007077103527 3.977914209143 5.081170168915 1 1 1 +C +0.0 +1 +4.779784174238 4.440311459394 4.230030312730 1 1 1 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/INPUT new file mode 100644 index 000000000..c3181c397 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS + +calculation md +atom_file STRU +kpoint_file KPT +pseudo_dir ./ +ntype 2 +symmetry 1 +ecutwfc 90 + +npool 1 + +mixing_type pulay +mixing_beta 0.4 + +nstep 3 +force_thr_ev 0.02 +#move_method cg +out_stru 0 +stress 1 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/INPUT new file mode 100644 index 000000000..63bd0ed40 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/INPUT @@ -0,0 +1,263 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +atom_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir .// #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +renormwithmesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional none #exchange correlation functional +calculation md #test; scf; relax; nscf; ienvelope; istate; +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +nbands 0 #number of bands +nbands_sto 0 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +nche_sto 0 #number of orders for Chebyshev expansion in stochastic DFT +symmetry 0 #turn symmetry on or off +set_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system + +#Parameters (2.PW) +ecutwfc 90 ##energy cutoff for wave functions +diago_cg_maxiter 50 #max iteration number for cg +diago_cg_prec 1 #diago_cg_prec +ethr 0.01 #threshold for eigenvalues is cg electron iterations +dr2 1e-09 #charge density error +start_wfc atomic #start wave functions are from 'atomic' or 'file' +start_charge atomic #start charge is from 'atomic' or file +charge_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_charge 0 #>0 output charge density for selected electron steps +out_potential 0 #output realspace potential +out_wf 0 #output wave functions +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Relaxation) +ks_solver cg #cg; dav; lapack; genelpa; hpseps; scalapack_gvx +niter 40 ##number of electron iterations +force_set 0 #output the force_set or not +nstep 3 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.00077787 #force threshold, unit: Ry/Bohr +force_thr_ev 0.02 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +cg_threshold 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +bfgs_w1 0.01 #wolfe condition 1 for bfgs +bfgs_w2 0.5 #wolfe condition 2 for bfgs +trust_radius_max 0.8 #maximal trust radius, unit: Bohr +trust_radius_min 1e-05 #minimal trust radius, unit: Bohr +trust_radius_ini 0.5 #initial trust radius, unit: Bohr +stress 1 #calculate the stress or not +fixed_axes None #which axes are fixed +move_method cg #bfgs; sd; cg; cg_bfgs; +out_level m #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +out_descriptor 0 #>0 compute descriptor for deepks +lmax_descriptor 2 #>0 lmax used in descriptor for deepks + +#Parameters (4.LCAO) +basis_type pw #PW; LCAO in pw; LCAO +new_dm 1 #Type of density matrix; 0: old 1: new +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 0 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_hs 0 #output H and S matrix +out_hs2 0 #output H(R) and S(R) matrix +out_r 0 #output r(R) matrix +out_lowf 0 #ouput LCAO wave functions +bx 1 #division of an element grid in FFT grid along x +by 1 #division of an element grid in FFT grid along y +bz 1 #division of an element grid in FFT grid along z + +#Parameters (5.Smearing) +smearing fixed #type of smearing: gauss; fd; fixed; mp; mp2; mv +sigma 0.01 #energy range for smearing + +#Parameters (6.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (7.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) + +#Parameters (8.Technique) +gamma_only 0 #gamma only, only used in LCAO basis +diago_proc 8 #number of proc used to diago +npool 1 #number of pools for k points, pw only +mem_saver 0 #memory saver for many k points used +printe 100 #print band energy for selectively ionic steps + +#Parameters (9.SIAO) +selinv_npole 40 #number of selected poles +selinv_temp 2000 #temperature for Fermi-Dirac distribution +selinv_gap 0 #supposed gap in the calculation +selinv_deltae 2 #expected energy range +selinv_mu -1 #chosen mu as Fermi energy +selinv_threshold 0.001 #threshold for calculated electron number +selinv_niter 50 #max number of steps to update mu + +#Parameters (10.Molecular dynamics) +md_mdtype 1 #choose ensemble +md_potential FP #choose potential +md_dt 1 #time step +mnhc 4 #number of Nose-Hoover chains +md_qmass 1 #mass of thermostat +md_tfirst 0 #temperature first +md_tlast 0 #temperature last +md_dumpmdfred 1 #The period to dump MD information for monitoring and restarting MD +md_mdoutpath mdoutput #output path of md +md_rstmd 0 #whether restart +md_fixtemperature 1 #period to change temperature +md_ediff 0.0001 #parameter for constraining total energy change +md_ediffg 0.001 #parameter for constraining max force change +NVT_tau 0 #parameter for adjust effect of thermostat +NVT_control 1 #choose which thermostat used in NVT ensemble +rcut_lj 8.5 #cutoff radius of LJ potential +epsilon_lj 0.01032 #the value of epsilon for LJ potential +sigma_lj 3.405 #the value of sigma for LJ potential + +#Parameters (11.Efield) +efield 0 #add electric field +edir 1 #add electric field +emaxpos 0.5 #maximal position of efield [0,1) +eopreg 0.1 #where sawlike potential decrease +eamp 0.001 #amplitute of the efield, unit is a.u. +eamp_v 0.05144 #amplitute of the efield, unit is V/A + +#Parameters (12.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vxc_in_h 1 #calculate the xc potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.Other Methods) +mlwf_flag 0 #turn MLWF on or off +opt_epsilon2 0 #calculate the dielectic function +opt_nbands 0 #number of bands for optical calculation + +#Parameters (14.VdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (15.spectrum) +spectral_type None #the type of the calculated spectrum +spectral_method 0 #0: tddft(linear response) +kernel_type rpa #the kernel type: rpa, tdlda ... +eels_method 0 #0: hilbert_transform method; 1: standard method +absorption_method 0 #0: vasp's method 1: pwscf's method +system bulk #the calculate system +eta 0.05 #eta(Ry) +domega 0.01 #domega(Ry) +nomega 300 #nomega +ecut_chi 1 #the dimension of chi matrix +q_start 0.1 0.1 0.1 #the position of the first q point in direct coordinate +q_direction 1 0 0 #the q direction +nq 1 #the total number of qpoints for calculation +out_epsilon 1 #output epsilon or not +out_chi 0 #output chi or not +out_chi0 0 #output chi0 or not +fermi_level 0 #the change of the fermi_level(Ry) +coulomb_cutoff 0 # turn on the coulomb_cutoff or not +kmesh_interpolation 0 #calculting +qcar 0 0 0 #(unit: 2PI/lat0) +ocp 0 #change occupation or not +ocp_set none #set occupation +lcao_box 10 10 10 #the scale for searching the existence of the overlap + mulliken 0 # mulliken charge or not +intrasmear 0 #Eta +shift 0 #shift +metalcalc 0 #metal or not +eps_degauss 0.01 #degauss in calculating epsilon0 +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction + +#Parameters (17.exx) +exx_hybrid_type no #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (17.tddft) +tddft 0 #calculate tddft or not +td_dr2 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not + +#Parameters (18.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice std::vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_MD b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_MD new file mode 100644 index 000000000..10302ea51 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_MD @@ -0,0 +1,27 @@ +ATOMIC_SPECIES +H 1.008 H_ONCV_PBE-1.0.upf +C 12.01 C_ONCV_PBE-1.0.upf + +LATTICE_CONSTANT +1.88972612546 + +LATTICE_VECTORS +9.70691437102 0 0 #latvec1 +-0.281382603073 9.68406871255 0 #latvec2 +0.158246266482 -0.163817668352 9.58297385826 #latvec3 + +ATOMIC_POSITIONS +Direct + +H #label +0 #magnetism +4 #number of atoms +0.535461381214 0.40022105074 0.350517908729 1 1 1 0 0 0 +0.384059480088 0.479432956913 0.433779873798 1 1 1 0 0 0 +0.553450272577 0.569838705306 0.439037455701 1 1 1 0 0 0 +0.521761060531 0.414199303256 0.541959017837 1 1 1 0 0 0 + +C #label +0 #magnetism +1 #number of atoms +0.498801629025 0.465841043252 0.44124373684 1 1 1 0 0 0 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_READIN_ADJUST.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 000000000..233b8c367 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.70691 +_cell_length_b 9.68815 +_cell_length_c 9.58568 +_cell_angle_alpha 91.0063 +_cell_angle_beta 89.0541 +_cell_angle_gamma 91.6643 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.53097 0.408053 0.361246 +H 0.398147 0.47768 0.434684 +H 0.54717 0.557856 0.43944 +H 0.51918 0.420134 0.530801 +C 0.498731 0.465842 0.441171 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_1.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_1.cif new file mode 100644 index 000000000..5a5b6ed05 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_1.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.70691 +_cell_length_b 9.68815 +_cell_length_c 9.58568 +_cell_angle_alpha 91.0063 +_cell_angle_beta 89.0541 +_cell_angle_gamma 91.6643 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.531666 0.406832 0.359568 +H 0.395926 0.477951 0.434543 +H 0.548145 0.559719 0.439384 +H 0.519578 0.419226 0.532529 +C 0.498744 0.465842 0.441183 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_2.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_2.cif new file mode 100644 index 000000000..898144995 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_2.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.70691 +_cell_length_b 9.68815 +_cell_length_c 9.58568 +_cell_angle_alpha 91.0063 +_cell_angle_beta 89.0541 +_cell_angle_gamma 91.6643 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.533403 0.403793 0.355398 +H 0.390433 0.478629 0.434192 +H 0.550578 0.564369 0.439236 +H 0.520575 0.416939 0.536854 +C 0.498773 0.465841 0.441212 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_3.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_3.cif new file mode 100644 index 000000000..a10888c1f --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/md_pos_3.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.70691 +_cell_length_b 9.68815 +_cell_length_c 9.58568 +_cell_angle_alpha 91.0063 +_cell_angle_beta 89.0541 +_cell_angle_gamma 91.6643 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.535461 0.400221 0.350518 +H 0.384059 0.479433 0.43378 +H 0.55345 0.569839 0.439037 +H 0.521761 0.414199 0.541959 +C 0.498802 0.465841 0.441244 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/running_md.log b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/running_md.log new file mode 100644 index 000000000..e60ae9ad2 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/OUT.ABACUS/running_md.log @@ -0,0 +1,701 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 8 + Start Time is Fri Nov 12 18:16:22 2021 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 8 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = H + atom label for species 2 = C + lattice constant (Bohr) = 1.88973 + lattice constant (Angstrom) = 1 + + READING ATOM TYPE 1 + atom label = H + L=0, number of zeta = 1 + L=1, number of zeta = 1 + L=2, number of zeta = 1 + number of atom for this type = 4 + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = C + L=0, number of zeta = 1 + L=1, number of zeta = 1 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + TOTAL ATOM NUMBER = 5 + + CARTESIAN COORDINATES ( UNIT = 1.88973 Bohr ). + atom x y z mag vx vy vz + tauc_H1 5.09642839721 3.89243558658 3.46181024571 0 0 0 0 + tauc_H2 3.79915812176 4.55467455263 4.16556354192 0 0 0 0 + tauc_H3 5.22389947082 5.33033053366 4.21113724544 0 0 0 0 + tauc_H4 5.00541687456 3.98165554454 5.08665008197 0 0 0 0 + tauc_C1 4.77987185192 4.43897624107 4.22772783445 0 0 0 0 + + + Volume (Bohr^3) = 6079.05350607 + Volume (A^3) = 900.821712756 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +9.70691437102 +0 +0 + -0.281382603073 +9.68406871255 +0 + +0.158246266482 -0.163817668352 +9.58297385826 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.103019349072 +0.00299335470133 -0.00165001629058 + -0 +0.10326238172 +0.0017652351819 + +0 -0 +0.104351740367 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is H_ONCV_PBE-1.0.upf + pseudopotential type = NC + functional Ex = PBE + functional Ec = + functional GCEx = + functional GCEc = + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is C_ONCV_PBE-1.0.upf + pseudopotential type = NC + functional Ex = PBE + functional Ec = + functional GCEx = + functional GCEc = + nonlocal core correction = 0 + valence electrons = 4 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + initial pseudo atomic orbital number = 0 + NLOCAL = 45 + + SETUP THE ELECTRONS NUMBER + electron number of element H = 1 + total electron number of element H = 4 + electron number of element C = 4 + total electron number of element C = 4 + occupied bands = 4 + NBANDS = 14 + DONE : SETUP UNITCELL Time : 0.070024178247 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0716588154319 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for wavefunc (unit:Ry) = 90 + [fft grid for wave functions] = 120, 120, 120 + [fft grid for charge/potential] = 120, 120, 120 + [fft grid division] = 1, 1, 1 + [big fft grid for charge/potential] = 120, 120, 120 + nbxx = 216000 + nrxx = 216000 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 701419 + number of sticks = 9633 + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + number of plane waves = 87687 + number of sticks = 2409 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 1204 87678 + 2 1204 87678 + 3 1205 87677 + 4 1204 87678 + 5 1204 87677 + 6 1204 87677 + 7 1204 87677 + 8 1204 87677 + --------------- sum ------------------- + 8 9633 701419 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(W) PW + 1 300 10959 + 2 301 10962 + 3 303 10960 + 4 302 10960 + 5 303 10961 + 6 300 10961 + 7 301 10964 + 8 299 10960 + --------------- sum ------------------- + 8 2409 87687 + + SETUP COORDINATES OF PLANE WAVES + number of total plane waves = 701419 + + SETUP COORDINATES OF PLANE WAVES + number of |g| = 84378 + max |g| = 32.563923009 + min |g| = 0 + DONE : INIT PLANEWAVE Time : 0.350538940344 (SEC) + + npwx = 10959 + + SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS + H non-local projectors: + projector 1 L=0 + projector 2 L=0 + C non-local projectors: + projector 1 L=0 + projector 2 L=0 + projector 3 L=1 + projector 4 L=1 + TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 + DONE : LOCAL POTENTIAL Time : 4.32109053986 (SEC) + + + Init Non-Local PseudoPotential table : + Init Non-Local-Pseudopotential done. + DONE : NON-LOCAL POTENTIAL Time : 4.32724457909 (SEC) + + start_pot = atomic + DONE : INIT POTENTIAL Time : 4.80582 (SEC) + + + Make real space PAO into reciprocal space. + max mesh points in Pseudopotential = 601 + dq(describe PAO in reciprocal space) = 0.01 + max q = 1143 + + number of pseudo atomic orbitals for H is 0 + + number of pseudo atomic orbitals for C is 0 + DONE : INIT BASIS Time : 5.09354 (SEC) + + ...............Nose-Hoover Chain parameter initialization............... + Temperature = 0 + Temperature2 = 0 + NHC frequency = 0.00120944 + NHC chain = 4 + Qmass = 1822.89 + ............................................................... + + PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + K-point CG iter num Time(Sec) + 1 9.785714 1.390000 + + Density error is 0.942995755677 + + PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + K-point CG iter num Time(Sec) + 1 2.285714 0.410000 + + Density error is 0.099685883319 + + PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + K-point CG iter num Time(Sec) + 1 4.142857 0.650000 + + Density error is 0.029031982042 + + PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + K-point CG iter num Time(Sec) + 1 4.285714 0.660000 + + Density error is 0.216126036110 + + PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + K-point CG iter num Time(Sec) + 1 3.357143 0.540000 + + Density error is 0.000141170928 + + PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + K-point CG iter num Time(Sec) + 1 7.357143 1.070000 + + Density error is 0.000036712166 + + PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + K-point CG iter num Time(Sec) + 1 3.928571 0.680000 + + Density error is 0.000012403136 + + PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + K-point CG iter num Time(Sec) + 1 4.642857 0.780000 + + Density error is 0.000000169540 + + PW ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + K-point CG iter num Time(Sec) + 1 6.785714 1.080000 + + Density error is 0.000000193385 + + PW ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + K-point CG iter num Time(Sec) + 1 4.000000 0.630000 + + Density error is 0.000000002471 + + PW ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + K-point CG iter num Time(Sec) + 1 9.000000 1.160000 + + Density error is 0.000000000287 + + charge density convergence is achieved + final etot is -219.132652714524 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +1.427623 -2.413519 -3.360832 + H2 -4.528626 +0.554349 -0.282580 + H3 +1.865702 +3.772834 -0.111599 + H4 +0.916683 -1.897685 +3.461780 + C1 +0.318617 -0.015979 +0.293231 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +10.529622 -0.107421 -0.098680 + -0.107421 +9.970420 +0.216130 + -0.098680 +0.216130 +9.886865 + +output Pressure for check! +Virtual Pressure is +20.257937 Kbar +Virial Term is +20.257937 Kbar +Kenetic Term is +0.000000 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 1 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -16.105947 (Rydberg) + NVT Temperature : +0.000000 (K) + NVT Kinetic energy : +0.000000 (Rydberg) + NVT Potential energy : -16.105947 (Rydberg) + maxForce : +0.007902 + maxStep : +0.041308 + MD_STEP SystemE Conserved DeltaE Temperature + +1 -8.052974 -8.052974 +0.000000 +171.583724 + + PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +54.428571 +6.400000 + + Density error is +0.003416963341 + + PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.214286 +0.340000 + + Density error is +0.000062315805 + + PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.071429 +0.560000 + + Density error is +0.000015787808 + + PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.357143 +0.480000 + + Density error is +0.000001288949 + + PW ALGORITHM --------------- ION=+2 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +5.500000 +0.750000 + + Density error is +0.000000182921 + + PW ALGORITHM --------------- ION=+2 ELEC=+6 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.857143 +0.420000 + + Density error is +0.000000016603 + + PW ALGORITHM --------------- ION=+2 ELEC=+7 -------------------------------- + K-point CG iter num Time(Sec) + +1 +5.285714 +0.700000 + + Density error is +0.000000011064 + + PW ALGORITHM --------------- ION=+2 ELEC=+8 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.330000 + + Density error is +0.000000004133 + + PW ALGORITHM --------------- ION=+2 ELEC=+9 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.214286 +0.470000 + + Density error is +0.000000000094 + + charge density convergence is achieved + final etot is -219.442104652403 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +1.068960 -1.799542 -2.503128 + H2 -3.353024 +0.414117 -0.209592 + H3 +1.397261 +2.832427 -0.092488 + H4 +0.691597 -1.440532 +2.608917 + C1 +0.195206 -0.006470 +0.196291 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +7.986919 -0.080516 -0.073538 + -0.080516 +7.635404 +0.126752 + -0.073538 +0.126752 +7.556286 + +output Pressure for check! +Virtual Pressure is +15.557594 Kbar +Virial Term is +15.452406 Kbar +Kenetic Term is +0.105188 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 2 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -16.108768 (Rydberg) + NVT Temperature : +524.091079 (K) + NVT Kinetic energy : +0.019916 (Rydberg) + NVT Potential energy : -16.128691 (Rydberg) + maxForce : +0.004333 + maxStep : +0.101848 + MD_STEP SystemE Conserved DeltaE Temperature + +2 -8.064346 -8.054384 +0.000000 +1059.261288 + + PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +56.071429 +6.530000 + + Density error is +0.019256453110 + + PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.214286 +0.340000 + + Density error is +0.000283272912 + + PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.214286 +0.570000 + + Density error is +0.000097131520 + + PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.714286 +0.400000 + + Density error is +0.000008019387 + + PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.642857 +0.630000 + + Density error is +0.000001180377 + + PW ALGORITHM --------------- ION=+3 ELEC=+6 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.571429 +0.500000 + + Density error is +0.000000049998 + + PW ALGORITHM --------------- ION=+3 ELEC=+7 -------------------------------- + K-point CG iter num Time(Sec) + +1 +5.500000 +0.740000 + + Density error is +0.000000005236 + + PW ALGORITHM --------------- ION=+3 ELEC=+8 -------------------------------- + K-point CG iter num Time(Sec) + +1 +5.285714 +0.690000 + + Density error is +0.000000019403 + + PW ALGORITHM --------------- ION=+3 ELEC=+9 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.571429 +0.390000 + + Density error is +0.000000001790 + + PW ALGORITHM --------------- ION=+3 ELEC=+10 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.000000 +0.550000 + + Density error is +0.000000000200 + + charge density convergence is achieved + final etot is -219.862372141037 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.332157 -0.540133 -0.744680 + H2 -0.978294 +0.129701 -0.061949 + H3 +0.426044 +0.880050 -0.050137 + H4 +0.219024 -0.477786 +0.818662 + C1 +0.001069 +0.008168 +0.038104 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +2.479531 -0.031426 -0.026005 + -0.031426 +2.489387 -0.034015 + -0.026005 -0.034015 +2.420180 + +output Pressure for check! +Virtual Pressure is +5.575435 Kbar +Virial Term is +4.926065 Kbar +Kenetic Term is +0.649370 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 3 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -16.111265 (Rydberg) + NVT Temperature : +1261.973956 (K) + NVT Kinetic energy : +0.047957 (Rydberg) + NVT Potential energy : -16.159581 (Rydberg) + maxForce : +0.000370 + maxStep : +0.117517 + MD_STEP SystemE Conserved DeltaE Temperature + +3 -8.079790 -8.055632 +0.000000 +1447.243804 + + + -------------------------------------------- + !FINAL_ETOT_IS -219.8623721410366443 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total +75.201 15 +5.01 +100.00 % + Run_pw plane_wave_line +75.18 1 +75.18 +99.97 % + PW_Basis gen_pw +0.28 1 +0.28 +0.37 % + Run_MD_PW md_cells_pw +74.83 1 +74.83 +99.51 % + ppcell_vl init_vloc +3.95 1 +3.95 +5.25 % + Potential init_pot +0.79 4 +0.20 +1.05 % + FFT FFT3D +28.10 8433 +0.00 +37.37 % + Charge atomic_rho +2.57 7 +0.37 +3.42 % + Potential v_of_rho +3.44 34 +0.10 +4.57 % + H_XC_pw v_xc +3.23 37 +0.09 +4.29 % + H_Hartree_pw v_hartree +0.42 34 +0.01 +0.56 % + wavefunc wfcinit +1.09 4 +0.27 +1.45 % + pp_cell_vnl getvnl +0.15 40 +0.00 +0.20 % + Hamilt_PW diagH_subspace +3.43 34 +0.10 +4.56 % + Hamilt_PW h_psi +29.25 3312 +0.01 +38.89 % + Hamilt_PW vloc +26.78 3312 +0.01 +35.61 % + Hamilt_PW vnl +2.38 3312 +0.00 +3.16 % + Hamilt_PW add_nonlocal_pp +1.01 3312 +0.00 +1.34 % + Run_MD_PW md_ions_pw +70.11 1 +70.11 +93.22 % + Electrons self_consistent +60.10 3 +20.03 +79.92 % + Electrons c_bands +31.03 30 +1.03 +41.27 % + Hamilt diagH_pw +30.90 30 +1.03 +41.09 % + Diago_CG diag +27.87 32 +0.87 +37.06 % + Charge sum_band +2.85 30 +0.10 +3.79 % + Charge rho_mpi +1.04 30 +0.03 +1.39 % + Charge mix_rho +0.97 30 +0.03 +1.29 % + Forces cal_force_nl +0.24 3 +0.08 +0.32 % + Stress_PW cal_stress +3.15 3 +1.05 +4.19 % + Stress_Func stress_ew +22.56 2 +11.28 +29.99 % + Force_Func stress_ew +22.55 2 +11.28 +29.99 % + Stress_Func stress_gga +0.13 3 +0.04 +0.17 % + Stress_Func stress_loc +1.37 3 +0.46 +1.82 % + Stress_Func stres_nl +1.54 3 +0.51 +2.05 % + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + +71.1170 + Charge_Pulay Rrho +13.1836 + Charge_Pulay dRrho +11.5356 + Charge_Pulay drho +11.5356 + Use_FFT porter +3.2959 + PW_Basis struc_fac +2.6757 + wavefunc evc +2.3411 + Charge rho +1.6479 + Charge rho_save +1.6479 + Charge rho_core +1.6479 + Potential vltot +1.6479 + Potential vr +1.6479 + Potential vr_eff +1.6479 + Potential vr_eff1 +1.6479 + Potential vnew +1.6479 + Charge_Pulay rho_save2 +1.6479 + ---------------------------------------------------------- + + Start Time : Fri Nov 12 18:16:22 2021 + Finish Time : Fri Nov 12 18:17:37 2021 + Total Time : 0 h 1 mins 15 secs diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/STRU b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/STRU new file mode 100644 index 000000000..07964f6fe --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000001/STRU @@ -0,0 +1,25 @@ +ATOMIC_SPECIES +H 1.008 H_ONCV_PBE-1.0.upf +C 12.010 C_ONCV_PBE-1.0.upf + +LATTICE_CONSTANT +1.8897261254578281 + +LATTICE_VECTORS +9.706914371019787 0.0 0.0 +-0.2813826030727322 9.684068712553056 0.0 +0.1582462664821918 -0.16381766835153533 9.582973858264781 + +ATOMIC_POSITIONS +Cartesian # Cartesian(Unit is LATTICE_CONSTANT) +H +0.0 +4 +5.096428397218 3.892435586573 3.461810245711 1 1 1 +3.799158121761 4.554674552629 4.165563541923 1 1 1 +5.223899470809 5.330330533668 4.211137245440 1 1 1 +5.005416874557 3.981655544542 5.086650081968 1 1 1 +C +0.0 +1 +4.779871851926 4.438976241080 4.227727834445 1 1 1 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/INPUT new file mode 100644 index 000000000..c3181c397 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/INPUT @@ -0,0 +1,20 @@ +INPUT_PARAMETERS + +calculation md +atom_file STRU +kpoint_file KPT +pseudo_dir ./ +ntype 2 +symmetry 1 +ecutwfc 90 + +npool 1 + +mixing_type pulay +mixing_beta 0.4 + +nstep 3 +force_thr_ev 0.02 +#move_method cg +out_stru 0 +stress 1 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/INPUT b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/INPUT new file mode 100644 index 000000000..63bd0ed40 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/INPUT @@ -0,0 +1,263 @@ +INPUT_PARAMETERS +#Parameters (1.General) +suffix ABACUS #the name of main output directory +latname test #the name of lattice name +atom_file STRU #the filename of file containing atom positions +kpoint_file KPT #the name of file containing k points +pseudo_dir .// #the directory containing pseudo files +orbital_dir #the directory containing orbital files +pseudo_type auto #the type pseudo files +pseudo_rcut 15 #cut-off radius for radial integration +renormwithmesh 0 #0: use our own mesh to do radial renormalization; 1: use mesh as in QE +lmaxmax 2 #maximum of l channels used +dft_functional none #exchange correlation functional +calculation md #test; scf; relax; nscf; ienvelope; istate; +ntype 2 #atom species number +nspin 1 #1: single spin; 2: up and down spin; 4: noncollinear spin +nbands 0 #number of bands +nbands_sto 0 #number of stochastic bands +nbands_istate 5 #number of bands around Fermi level for istate calulation +nche_sto 0 #number of orders for Chebyshev expansion in stochastic DFT +symmetry 0 #turn symmetry on or off +set_vel 0 #read velocity from STRU or not +symmetry_prec 1e-05 #accuracy for symmetry +nelec 0 #input number of electrons +tot_magnetization 0 #total magnetization of the system + +#Parameters (2.PW) +ecutwfc 90 ##energy cutoff for wave functions +diago_cg_maxiter 50 #max iteration number for cg +diago_cg_prec 1 #diago_cg_prec +ethr 0.01 #threshold for eigenvalues is cg electron iterations +dr2 1e-09 #charge density error +start_wfc atomic #start wave functions are from 'atomic' or 'file' +start_charge atomic #start charge is from 'atomic' or file +charge_extrap atomic #atomic; first-order; second-order; dm:coefficients of SIA +out_charge 0 #>0 output charge density for selected electron steps +out_potential 0 #output realspace potential +out_wf 0 #output wave functions +out_dos 0 #output energy and dos +out_band 0 #output energy and band structure +restart_save 0 #print to disk every step for restart +restart_load 0 #restart from disk +read_file_dir auto #directory of files for reading +nx 0 #number of points along x axis for FFT grid +ny 0 #number of points along y axis for FFT grid +nz 0 #number of points along z axis for FFT grid +cell_factor 1.2 #used in the construction of the pseudopotential tables + +#Parameters (3.Relaxation) +ks_solver cg #cg; dav; lapack; genelpa; hpseps; scalapack_gvx +niter 40 ##number of electron iterations +force_set 0 #output the force_set or not +nstep 3 #number of ion iteration steps +out_stru 0 #output the structure files after each ion step +force_thr 0.00077787 #force threshold, unit: Ry/Bohr +force_thr_ev 0.02 #force threshold, unit: eV/Angstrom +force_thr_ev2 0 #force invalid threshold, unit: eV/Angstrom +cg_threshold 0.5 #threshold for switching from cg to bfgs, unit: eV/Angstrom +stress_thr 0.01 #stress threshold +press1 0 #target pressure, unit: KBar +press2 0 #target pressure, unit: KBar +press3 0 #target pressure, unit: KBar +bfgs_w1 0.01 #wolfe condition 1 for bfgs +bfgs_w2 0.5 #wolfe condition 2 for bfgs +trust_radius_max 0.8 #maximal trust radius, unit: Bohr +trust_radius_min 1e-05 #minimal trust radius, unit: Bohr +trust_radius_ini 0.5 #initial trust radius, unit: Bohr +stress 1 #calculate the stress or not +fixed_axes None #which axes are fixed +move_method cg #bfgs; sd; cg; cg_bfgs; +out_level m #ie(for electrons); i(for ions); +out_dm 0 #>0 output density matrix +out_descriptor 0 #>0 compute descriptor for deepks +lmax_descriptor 2 #>0 lmax used in descriptor for deepks + +#Parameters (4.LCAO) +basis_type pw #PW; LCAO in pw; LCAO +new_dm 1 #Type of density matrix; 0: old 1: new +search_radius -1 #input search radius (Bohr) +search_pbc 1 #input periodic boundary condition +lcao_ecut 0 #energy cutoff for LCAO +lcao_dk 0.01 #delta k for 1D integration in LCAO +lcao_dr 0.01 #delta r for 1D integration in LCAO +lcao_rmax 30 #max R for 1D two-center integration table +out_hs 0 #output H and S matrix +out_hs2 0 #output H(R) and S(R) matrix +out_r 0 #output r(R) matrix +out_lowf 0 #ouput LCAO wave functions +bx 1 #division of an element grid in FFT grid along x +by 1 #division of an element grid in FFT grid along y +bz 1 #division of an element grid in FFT grid along z + +#Parameters (5.Smearing) +smearing fixed #type of smearing: gauss; fd; fixed; mp; mp2; mv +sigma 0.01 #energy range for smearing + +#Parameters (6.Charge Mixing) +mixing_type pulay #plain; kerker; pulay; pulay-kerker; broyden +mixing_beta 0.4 #mixing parameter: 0 means no new charge +mixing_ndim 8 #mixing dimension in pulay +mixing_gg0 0 #mixing parameter in kerker + +#Parameters (7.DOS) +dos_emin_ev -15 #minimal range for dos +dos_emax_ev 15 #maximal range for dos +dos_edelta_ev 0.01 #delta energy for dos +dos_scale 0.01 #scale dos range by +dos_sigma 0.07 #gauss b coefficeinet(default=0.07) + +#Parameters (8.Technique) +gamma_only 0 #gamma only, only used in LCAO basis +diago_proc 8 #number of proc used to diago +npool 1 #number of pools for k points, pw only +mem_saver 0 #memory saver for many k points used +printe 100 #print band energy for selectively ionic steps + +#Parameters (9.SIAO) +selinv_npole 40 #number of selected poles +selinv_temp 2000 #temperature for Fermi-Dirac distribution +selinv_gap 0 #supposed gap in the calculation +selinv_deltae 2 #expected energy range +selinv_mu -1 #chosen mu as Fermi energy +selinv_threshold 0.001 #threshold for calculated electron number +selinv_niter 50 #max number of steps to update mu + +#Parameters (10.Molecular dynamics) +md_mdtype 1 #choose ensemble +md_potential FP #choose potential +md_dt 1 #time step +mnhc 4 #number of Nose-Hoover chains +md_qmass 1 #mass of thermostat +md_tfirst 0 #temperature first +md_tlast 0 #temperature last +md_dumpmdfred 1 #The period to dump MD information for monitoring and restarting MD +md_mdoutpath mdoutput #output path of md +md_rstmd 0 #whether restart +md_fixtemperature 1 #period to change temperature +md_ediff 0.0001 #parameter for constraining total energy change +md_ediffg 0.001 #parameter for constraining max force change +NVT_tau 0 #parameter for adjust effect of thermostat +NVT_control 1 #choose which thermostat used in NVT ensemble +rcut_lj 8.5 #cutoff radius of LJ potential +epsilon_lj 0.01032 #the value of epsilon for LJ potential +sigma_lj 3.405 #the value of sigma for LJ potential + +#Parameters (11.Efield) +efield 0 #add electric field +edir 1 #add electric field +emaxpos 0.5 #maximal position of efield [0,1) +eopreg 0.1 #where sawlike potential decrease +eamp 0.001 #amplitute of the efield, unit is a.u. +eamp_v 0.05144 #amplitute of the efield, unit is V/A + +#Parameters (12.Test) +out_alllog 0 #output information for each processor, when parallel +nurse 0 #for coders +colour 0 #for coders, make their live colourful +t_in_h 1 #calculate the kinetic energy or not +vl_in_h 1 #calculate the local potential or not +vnl_in_h 1 #calculate the nonlocal potential or not +vh_in_h 1 #calculate the hartree potential or not +vxc_in_h 1 #calculate the xc potential or not +vion_in_h 1 #calculate the local ionic potential or not +test_force 0 #test the force +test_stress 0 #test the force + +#Parameters (13.Other Methods) +mlwf_flag 0 #turn MLWF on or off +opt_epsilon2 0 #calculate the dielectic function +opt_nbands 0 #number of bands for optical calculation + +#Parameters (14.VdW Correction) +vdw_method none #the method of calculating vdw (none ; d2 ; d3_0 ; d3_bj +vdw_s6 default #scale parameter of d2/d3_0/d3_bj +vdw_s8 default #scale parameter of d3_0/d3_bj +vdw_a1 default #damping parameter of d3_0/d3_bj +vdw_a2 default #damping parameter of d3_bj +vdw_d 20 #damping parameter of d2 +vdw_abc 0 #third-order term? +vdw_C6_file default #filename of C6 +vdw_C6_unit Jnm6/mol #unit of C6, Jnm6/mol or eVA6 +vdw_R0_file default #filename of R0 +vdw_R0_unit A #unit of R0, A or Bohr +vdw_model radius #expression model of periodic structure, radius or period +vdw_radius default #radius cutoff for periodic structure +vdw_radius_unit Bohr #unit of radius cutoff for periodic structure +vdw_cn_thr 40 #radius cutoff for cn +vdw_cn_thr_unit Bohr #unit of cn_thr, Bohr or Angstrom +vdw_period 3 3 3 #periods of periodic structure + +#Parameters (15.spectrum) +spectral_type None #the type of the calculated spectrum +spectral_method 0 #0: tddft(linear response) +kernel_type rpa #the kernel type: rpa, tdlda ... +eels_method 0 #0: hilbert_transform method; 1: standard method +absorption_method 0 #0: vasp's method 1: pwscf's method +system bulk #the calculate system +eta 0.05 #eta(Ry) +domega 0.01 #domega(Ry) +nomega 300 #nomega +ecut_chi 1 #the dimension of chi matrix +q_start 0.1 0.1 0.1 #the position of the first q point in direct coordinate +q_direction 1 0 0 #the q direction +nq 1 #the total number of qpoints for calculation +out_epsilon 1 #output epsilon or not +out_chi 0 #output chi or not +out_chi0 0 #output chi0 or not +fermi_level 0 #the change of the fermi_level(Ry) +coulomb_cutoff 0 # turn on the coulomb_cutoff or not +kmesh_interpolation 0 #calculting +qcar 0 0 0 #(unit: 2PI/lat0) +ocp 0 #change occupation or not +ocp_set none #set occupation +lcao_box 10 10 10 #the scale for searching the existence of the overlap + mulliken 0 # mulliken charge or not +intrasmear 0 #Eta +shift 0 #shift +metalcalc 0 #metal or not +eps_degauss 0.01 #degauss in calculating epsilon0 +noncolin 0 #using non-collinear-spin +lspinorb 0 #consider the spin-orbit interaction + +#Parameters (17.exx) +exx_hybrid_type no #no, hf, pbe0, hse or opt_orb +exx_hybrid_alpha 0.25 # +exx_hse_omega 0.11 # +exx_separate_loop 1 #0 or 1 +exx_hybrid_step 100 # +exx_lambda 0.3 # +exx_pca_threshold 0 # +exx_c_threshold 0 # +exx_v_threshold 0 # +exx_dm_threshold 0 # +exx_schwarz_threshold0 # +exx_cauchy_threshold0 # +exx_ccp_threshold 1e-08 # +exx_ccp_rmesh_times 10 # +exx_distribute_type htime #htime or kmeans1 or kmeans2 +exx_opt_orb_lmax 0 # +exx_opt_orb_ecut 0 # +exx_opt_orb_tolerence0 # + +#Parameters (17.tddft) +tddft 0 #calculate tddft or not +td_dr2 1e-09 #threshold for electronic iteration of tddft +td_dt 0.02 #time of ion step +td_force_dt 0.02 #time of force change +td_val_elec_01 1 #td_val_elec_01 +td_val_elec_02 1 #td_val_elec_02 +td_val_elec_03 1 #td_val_elec_03 +td_vext 0 #add extern potential or not +td_vext_dire 1 #extern potential direction +td_timescale 0.5 #extern potential td_timescale +td_vexttype 1 #extern potential type +td_vextout 0 #output extern potential or not +td_dipoleout 0 #output dipole or not + +#Parameters (18.berry_wannier) +berry_phase 0 #calculate berry phase or not +gdir 3 #calculate the polarization in the direction of the lattice std::vector +towannier90 0 #use wannier90 code interface or not +nnkpfile seedname.nnkp #the wannier90 code nnkp file name +wannier_spin up #calculate spin in wannier90 code interface diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_MD b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_MD new file mode 100644 index 000000000..f42357382 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_MD @@ -0,0 +1,27 @@ +ATOMIC_SPECIES +H 1.008 H_ONCV_PBE-1.0.upf +C 12.01 C_ONCV_PBE-1.0.upf + +LATTICE_CONSTANT +1.88972612546 + +LATTICE_VECTORS +9.27069258481 0 0 #latvec1 +0.0128238456952 9.56209520274 0 #latvec2 +0.169560774735 -0.0300305282636 9.58609795568 #latvec3 + +ATOMIC_POSITIONS +Direct + +H #label +0 #magnetism +4 #number of atoms +0.547461705223 0.400166750312 0.349585199322 1 1 1 0 0 0 +0.387154932277 0.478943964961 0.433851040704 1 1 1 0 0 0 +0.560703231408 0.571623190735 0.438580636423 1 1 1 0 0 0 +0.532932139137 0.411873023092 0.541312594704 1 1 1 0 0 0 + +C #label +0 #magnetism +1 #number of atoms +0.507726212428 0.465642779417 0.440714011322 1 1 1 0 0 0 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_READIN_ADJUST.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_READIN_ADJUST.cif new file mode 100644 index 000000000..6d8352991 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/STRU_READIN_ADJUST.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.27069 +_cell_length_b 9.5621 +_cell_length_c 9.58764 +_cell_angle_alpha 90.1781 +_cell_angle_beta 88.9867 +_cell_angle_gamma 89.9232 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.542192 0.408202 0.360768 +H 0.401673 0.477208 0.434698 +H 0.554241 0.559124 0.439031 +H 0.529933 0.417895 0.530426 +C 0.507735 0.465662 0.44058 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_1.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_1.cif new file mode 100644 index 000000000..bd632634b --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_1.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.27069 +_cell_length_b 9.5621 +_cell_length_c 9.58764 +_cell_angle_alpha 90.1781 +_cell_angle_beta 88.9867 +_cell_angle_gamma 89.9232 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.543005 0.406936 0.359006 +H 0.399395 0.477474 0.434569 +H 0.555241 0.561082 0.43897 +H 0.530384 0.416975 0.532107 +C 0.507737 0.465659 0.440603 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_2.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_2.cif new file mode 100644 index 000000000..724fd225e --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_2.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.27069 +_cell_length_b 9.5621 +_cell_length_c 9.58764 +_cell_angle_alpha 90.1781 +_cell_angle_beta 88.9867 +_cell_angle_gamma 89.9232 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.545037 0.403807 0.354649 +H 0.393743 0.47814 0.434243 +H 0.55774 0.565945 0.438806 +H 0.53153 0.414656 0.536324 +C 0.507736 0.465651 0.440656 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_3.cif b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_3.cif new file mode 100644 index 000000000..659d52e66 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/md_pos_3.cif @@ -0,0 +1,24 @@ +data_test + +_audit_creation_method generated by ABACUS + +_cell_length_a 9.27069 +_cell_length_b 9.5621 +_cell_length_c 9.58764 +_cell_angle_alpha 90.1781 +_cell_angle_beta 88.9867 +_cell_angle_gamma 89.9232 + +_symmetry_space_group_name_H-M +_symmetry_Int_Tables_number + +loop_ +_atom_site_label +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +H 0.547462 0.400167 0.349585 +H 0.387155 0.478944 0.433851 +H 0.560703 0.571623 0.438581 +H 0.532932 0.411873 0.541313 +C 0.507726 0.465643 0.440714 diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/running_md.log b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/running_md.log new file mode 100644 index 000000000..2a1ad64a8 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/OUT.ABACUS/running_md.log @@ -0,0 +1,701 @@ + + WELCOME TO ABACUS + + 'Atomic-orbital Based Ab-initio Computation at UStc' + + Website: http://abacus.ustc.edu.cn/ + + Version: Parallel, in development + Processor Number is 8 + Start Time is Fri Nov 12 18:17:38 2021 + + ------------------------------------------------------------------------------------ + + READING GENERAL INFORMATION + global_out_dir = OUT.ABACUS/ + global_in_card = INPUT + pseudo_dir = + orbital_dir = + pseudo_type = auto + DRANK = 1 + DSIZE = 8 + DCOLOR = 1 + GRANK = 1 + GSIZE = 1 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading atom information in unitcell: | + | From the input file and the structure file we know the number of | + | different elments in this unitcell, then we list the detail | + | information for each element, especially the zeta and polar atomic | + | orbital number for each element. The total atom number is counted. | + | We calculate the nearest atom distance for each atom and show the | + | Cartesian and Direct coordinates for each atom. We list the file | + | address for atomic orbitals. The volume and the lattice vectors | + | in real and reciprocal space is also shown. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + READING UNITCELL INFORMATION + ntype = 2 + atom label for species 1 = H + atom label for species 2 = C + lattice constant (Bohr) = 1.88973 + lattice constant (Angstrom) = 1 + + READING ATOM TYPE 1 + atom label = H + L=0, number of zeta = 1 + L=1, number of zeta = 1 + L=2, number of zeta = 1 + number of atom for this type = 4 + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + start magnetization = FALSE + + READING ATOM TYPE 2 + atom label = C + L=0, number of zeta = 1 + L=1, number of zeta = 1 + L=2, number of zeta = 1 + number of atom for this type = 1 + start magnetization = FALSE + + TOTAL ATOM NUMBER = 5 + + CARTESIAN COORDINATES ( UNIT = 1.88973 Bohr ). + atom x y z mag vx vy vz + tauc_H1 5.09290605164 3.89242871555 3.45835777937 0 0 0 0 + tauc_H2 3.80361094208 4.55005711875 4.16705754763 0 0 0 0 + tauc_H3 5.21981288147 5.33321039636 4.20859510266 0 0 0 0 + tauc_H4 5.00814830724 3.9800234484 5.08471194545 0 0 0 0 + tauc_C1 4.78773457902 4.43947390549 4.22344175994 0 0 0 0 + + + Volume (Bohr^3) = 5734.60762332 + Volume (A^3) = 849.780160031 + + Lattice vectors: (Cartesian coordinate: in unit of a_0) + +9.27069258481 +0 +0 + +0.0128238456952 +9.56209520274 +0 + +0.169560774735 -0.0300305282636 +9.58609795568 + Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0) + +0.107866806158 -0.000144661525376 -0.001908422339 + -0 +0.104579590435 +0.000327618219725 + +0 +0 +0.104317732264 + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Reading pseudopotentials files: | + | The pseudopotential file is in UPF format. The 'NC' indicates that | + | the type of pseudopotential is 'norm conserving'. Functional of | + | exchange and correlation is decided by 4 given parameters in UPF | + | file. We also read in the 'core correction' if there exists. | + | Also we can read the valence electrons number and the maximal | + | angular momentum used in this pseudopotential. We also read in the | + | trail wave function, trail atomic density and local-pseudopotential| + | on logrithmic grid. The non-local pseudopotential projector is also| + | read in if there is any. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is H_ONCV_PBE-1.0.upf + pseudopotential type = NC + functional Ex = PBE + functional Ec = + functional GCEx = + functional GCEc = + nonlocal core correction = 0 + valence electrons = 1 + lmax = 0 + number of zeta = 0 + number of projectors = 2 + L of projector = 0 + L of projector = 0 + PAO radial cut off (Bohr) = 15 + + Read in pseudopotential file is C_ONCV_PBE-1.0.upf + pseudopotential type = NC + functional Ex = PBE + functional Ec = + functional GCEx = + functional GCEc = + nonlocal core correction = 0 + valence electrons = 4 + lmax = 1 + number of zeta = 0 + number of projectors = 4 + L of projector = 0 + L of projector = 0 + L of projector = 1 + L of projector = 1 + initial pseudo atomic orbital number = 0 + NLOCAL = 45 + + SETUP THE ELECTRONS NUMBER + electron number of element H = 1 + total electron number of element H = 4 + electron number of element C = 4 + total electron number of element C = 4 + occupied bands = 4 + NBANDS = 14 + DONE : SETUP UNITCELL Time : 0.0822040801286 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup K-points | + | We setup the k-points according to input parameters. | + | The reduced k-points are set according to symmetry operations. | + | We treat the spin as another set of k-points. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP K-POINTS + nspin = 1 + Input type of k points = Monkhorst-Pack(Gamma) + nkstot = 1 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 1 + + k-point number in this process = 1 + minimum distributed K point number = 1 + + KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z WEIGHT + 1 0 0 0 2 + + KPOINTS DIRECT_X DIRECT_Y DIRECT_Z WEIGHT + 1 0 0 0 2 + DONE : INIT K-POINTS Time : 0.0836835908704 (SEC) + + + + + + >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> + | | + | Setup plane waves: | + | Use the energy cutoff and the lattice vectors to generate the | + | dimensions of FFT grid. The number of FFT grid on each processor | + | is 'nrxx'. The number of plane wave basis in reciprocal space is | + | different for charege/potential and wave functions. We also set | + | the 'sticks' for the parallel of FFT. | + | | + <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + + + + SETUP THE PLANE WAVE BASIS + energy cutoff for wavefunc (unit:Ry) = 90 + [fft grid for wave functions] = 108, 120, 120 + [fft grid for charge/potential] = 108, 120, 120 + [fft grid division] = 1, 1, 1 + [big fft grid for charge/potential] = 108, 120, 120 + nbxx = 194400 + nrxx = 194400 + + SETUP PLANE WAVES FOR CHARGE/POTENTIAL + number of plane waves = 661353 + number of sticks = 9057 + + SETUP PLANE WAVES FOR WAVE FUNCTIONS + number of plane waves = 82689 + number of sticks = 2267 + + PARALLEL PW FOR CHARGE/POTENTIAL + PROC COLUMNS(POT) PW + 1 1132 82670 + 2 1132 82669 + 3 1132 82669 + 4 1132 82669 + 5 1132 82669 + 6 1132 82669 + 7 1133 82669 + 8 1132 82669 + --------------- sum ------------------- + 8 9057 661353 + + PARALLEL PW FOR WAVE FUNCTIONS + PROC COLUMNS(W) PW + 1 284 10334 + 2 283 10336 + 3 283 10338 + 4 281 10335 + 5 285 10338 + 6 285 10336 + 7 282 10334 + 8 284 10338 + --------------- sum ------------------- + 8 2267 82689 + + SETUP COORDINATES OF PLANE WAVES + number of total plane waves = 661353 + + SETUP COORDINATES OF PLANE WAVES + number of |g| = 79694 + max |g| = 32.5641662388 + min |g| = 0 + DONE : INIT PLANEWAVE Time : 0.336783995619 (SEC) + + npwx = 10334 + + SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS + H non-local projectors: + projector 1 L=0 + projector 2 L=0 + C non-local projectors: + projector 1 L=0 + projector 2 L=0 + projector 3 L=1 + projector 4 L=1 + TOTAL NUMBER OF NONLOCAL PROJECTORS = 16 + DONE : LOCAL POTENTIAL Time : 4.04769805988 (SEC) + + + Init Non-Local PseudoPotential table : + Init Non-Local-Pseudopotential done. + DONE : NON-LOCAL POTENTIAL Time : 4.05365722452 (SEC) + + start_pot = atomic + DONE : INIT POTENTIAL Time : 4.48892 (SEC) + + + Make real space PAO into reciprocal space. + max mesh points in Pseudopotential = 601 + dq(describe PAO in reciprocal space) = 0.01 + max q = 1143 + + number of pseudo atomic orbitals for H is 0 + + number of pseudo atomic orbitals for C is 0 + DONE : INIT BASIS Time : 4.74304 (SEC) + + ...............Nose-Hoover Chain parameter initialization............... + Temperature = 0 + Temperature2 = 0 + NHC frequency = 0.00120944 + NHC chain = 4 + Qmass = 1822.89 + ............................................................... + + PW ALGORITHM --------------- ION= 1 ELEC= 1-------------------------------- + K-point CG iter num Time(Sec) + 1 10.000000 1.100000 + + Density error is 0.960510453558 + + PW ALGORITHM --------------- ION= 1 ELEC= 2-------------------------------- + K-point CG iter num Time(Sec) + 1 2.285714 0.310000 + + Density error is 0.098733734228 + + PW ALGORITHM --------------- ION= 1 ELEC= 3-------------------------------- + K-point CG iter num Time(Sec) + 1 4.071429 0.500000 + + Density error is 0.029156016548 + + PW ALGORITHM --------------- ION= 1 ELEC= 4-------------------------------- + K-point CG iter num Time(Sec) + 1 3.714286 0.450000 + + Density error is 0.157357850345 + + PW ALGORITHM --------------- ION= 1 ELEC= 5-------------------------------- + K-point CG iter num Time(Sec) + 1 3.142857 0.390000 + + Density error is 0.000022976111 + + PW ALGORITHM --------------- ION= 1 ELEC= 6-------------------------------- + K-point CG iter num Time(Sec) + 1 8.785714 0.970000 + + Density error is 0.000027903812 + + PW ALGORITHM --------------- ION= 1 ELEC= 7-------------------------------- + K-point CG iter num Time(Sec) + 1 4.357143 0.530000 + + Density error is 0.000007318066 + + PW ALGORITHM --------------- ION= 1 ELEC= 8-------------------------------- + K-point CG iter num Time(Sec) + 1 5.000000 0.590000 + + Density error is 0.000000148874 + + PW ALGORITHM --------------- ION= 1 ELEC= 9-------------------------------- + K-point CG iter num Time(Sec) + 1 6.428571 0.730000 + + Density error is 0.000000001372 + + PW ALGORITHM --------------- ION= 1 ELEC= 10-------------------------------- + K-point CG iter num Time(Sec) + 1 7.714286 0.860000 + + Density error is 0.000000001003 + + PW ALGORITHM --------------- ION= 1 ELEC= 11-------------------------------- + K-point CG iter num Time(Sec) + 1 7.785714 0.880000 + + Density error is 0.000000000059 + + charge density convergence is achieved + final etot is -219.118728218927 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +1.508322 -2.517782 -3.530747 + H2 -4.418462 +0.530736 -0.259007 + H3 +1.940423 +3.914120 -0.121649 + H4 +0.930235 -1.848593 +3.369226 + C1 +0.039482 -0.078480 +0.542177 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +11.019212 -0.012921 -0.249753 + -0.012921 +10.888803 +0.464085 + -0.249753 +0.464085 +10.579625 + +output Pressure for check! +Virtual Pressure is +21.658426 Kbar +Virial Term is +21.658426 Kbar +Kenetic Term is +0.000000 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 1 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -16.104924 (Rydberg) + NVT Temperature : +0.000000 (K) + NVT Kinetic energy : +0.000000 (Rydberg) + NVT Potential energy : -16.104924 (Rydberg) + maxForce : +0.007972 + maxStep : +0.041509 + MD_STEP SystemE Conserved DeltaE Temperature + +1 -8.052462 -8.052462 +0.000000 +175.027577 + + PW ALGORITHM --------------- ION=+2 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +55.142857 +5.680000 + + Density error is +0.003488598323 + + PW ALGORITHM --------------- ION=+2 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.214286 +0.300000 + + Density error is +0.000064088512 + + PW ALGORITHM --------------- ION=+2 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.071429 +0.480000 + + Density error is +0.000016147980 + + PW ALGORITHM --------------- ION=+2 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.214286 +0.410000 + + Density error is +0.000001278683 + + PW ALGORITHM --------------- ION=+2 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +5.071429 +0.600000 + + Density error is +0.000000184850 + + PW ALGORITHM --------------- ION=+2 ELEC=+6 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.214286 +0.410000 + + Density error is +0.000000013531 + + PW ALGORITHM --------------- ION=+2 ELEC=+7 -------------------------------- + K-point CG iter num Time(Sec) + +1 +5.285714 +0.610000 + + Density error is +0.000000010165 + + PW ALGORITHM --------------- ION=+2 ELEC=+8 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.000000 +0.290000 + + Density error is +0.000000003623 + + PW ALGORITHM --------------- ION=+2 ELEC=+9 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.928571 +0.370000 + + Density error is +0.000000000004 + + charge density convergence is achieved + final etot is -219.434191715312 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +1.133157 -1.856662 -2.608308 + H2 -3.288841 +0.401876 -0.196306 + H3 +1.454909 +2.915560 -0.103398 + H4 +0.716634 -1.407419 +2.547272 + C1 -0.015860 -0.053356 +0.360740 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +8.401340 -0.025640 -0.170148 + -0.025640 +8.286073 +0.280673 + -0.170148 +0.280673 +8.068639 + +output Pressure for check! +Virtual Pressure is +16.617778 Kbar +Virial Term is +16.504034 Kbar +Kenetic Term is +0.113744 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 2 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -16.107810 (Rydberg) + NVT Temperature : +533.989848 (K) + NVT Kinetic energy : +0.020293 (Rydberg) + NVT Potential energy : -16.128110 (Rydberg) + maxForce : +0.004362 + maxStep : +0.102614 + MD_STEP SystemE Conserved DeltaE Temperature + +2 -8.064055 -8.053905 +0.000000 +1078.821137 + + PW ALGORITHM --------------- ION=+3 ELEC=+1 -------------------------------- + K-point CG iter num Time(Sec) + +1 +53.785714 +5.530000 + + Density error is +0.019612648889 + + PW ALGORITHM --------------- ION=+3 ELEC=+2 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.214286 +0.300000 + + Density error is +0.000290072895 + + PW ALGORITHM --------------- ION=+3 ELEC=+3 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.142857 +0.490000 + + Density error is +0.000099169017 + + PW ALGORITHM --------------- ION=+3 ELEC=+4 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.714286 +0.350000 + + Density error is +0.000008092362 + + PW ALGORITHM --------------- ION=+3 ELEC=+5 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.428571 +0.530000 + + Density error is +0.000001211193 + + PW ALGORITHM --------------- ION=+3 ELEC=+6 -------------------------------- + K-point CG iter num Time(Sec) + +1 +3.357143 +0.420000 + + Density error is +0.000000051304 + + PW ALGORITHM --------------- ION=+3 ELEC=+7 -------------------------------- + K-point CG iter num Time(Sec) + +1 +5.500000 +0.630000 + + Density error is +0.000000007503 + + PW ALGORITHM --------------- ION=+3 ELEC=+8 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.857143 +0.580000 + + Density error is +0.000000014633 + + PW ALGORITHM --------------- ION=+3 ELEC=+9 -------------------------------- + K-point CG iter num Time(Sec) + +1 +2.214286 +0.300000 + + Density error is +0.000000002243 + + PW ALGORITHM --------------- ION=+3 ELEC=+10 -------------------------------- + K-point CG iter num Time(Sec) + +1 +4.142857 +0.500000 + + Density error is +0.000000000398 + + charge density convergence is achieved + final etot is -219.861273145100 eV + + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-FORCE (eV/Angstrom) + + ><><><><><><><><><><><><><><><><><><><><><>< + + atom x y z + H1 +0.370637 -0.522900 -0.745579 + H2 -0.985036 +0.136881 -0.067108 + H3 +0.457129 +0.867257 -0.061860 + H4 +0.261706 -0.471416 +0.808625 + C1 -0.104436 -0.009822 +0.065922 + + + ><><><><><><><><><><><><><><><><><><><><><>< + + TOTAL-STRESS (KBAR) + + ><><><><><><><><><><><><><><><><><><><><><>< + + +2.700073 -0.048954 -0.024676 + -0.048954 +2.601966 -0.047102 + -0.024676 -0.047102 +2.553528 + +output Pressure for check! +Virtual Pressure is +5.938130 Kbar +Virial Term is +5.237045 Kbar +Kenetic Term is +0.701085 Kbar + + -------------------------------------------------- + Molecular Dynamics (NVT) STEP 3 + -------------------------------------------------- +-------------------------------------------------- + SUMMARY OF NVT CALCULATION + -------------------------------------------------- + NVT Conservation : -16.110343 (Rydberg) + NVT Temperature : +1283.993234 (K) + NVT Kinetic energy : +0.048794 (Rydberg) + NVT Potential energy : -16.159500 (Rydberg) + maxForce : +0.000376 + maxStep : +0.119327 + MD_STEP SystemE Conserved DeltaE Temperature + +3 -8.079750 -8.055171 +0.000000 +1471.487172 + + + -------------------------------------------- + !FINAL_ETOT_IS -219.8612731451002276 eV + -------------------------------------------- + + + + + + + |CLASS_NAME---------|NAME---------------|TIME(Sec)-----|CALLS----|AVG------|PER%------- + total +68.402 15 +4.56 +100.00 % + Run_pw plane_wave_line +68.38 1 +68.38 +99.97 % + PW_Basis gen_pw +0.25 1 +0.25 +0.37 % + Run_MD_PW md_cells_pw +68.05 1 +68.05 +99.48 % + ppcell_vl init_vloc +3.69 1 +3.69 +5.39 % + Potential init_pot +0.71 4 +0.18 +1.04 % + FFT FFT3D +23.26 8449 +0.00 +34.00 % + Charge atomic_rho +2.26 7 +0.32 +3.31 % + Potential v_of_rho +3.00 34 +0.09 +4.38 % + H_XC_pw v_xc +2.82 37 +0.08 +4.13 % + H_Hartree_pw v_hartree +0.36 34 +0.01 +0.53 % + wavefunc wfcinit +0.99 4 +0.25 +1.44 % + pp_cell_vnl getvnl +0.14 40 +0.00 +0.20 % + Hamilt_PW diagH_subspace +2.84 34 +0.08 +4.15 % + Hamilt_PW h_psi +24.69 3320 +0.01 +36.09 % + Hamilt_PW vloc +22.48 3320 +0.01 +32.86 % + Hamilt_PW vnl +2.12 3320 +0.00 +3.10 % + Hamilt_PW add_nonlocal_pp +0.94 3320 +0.00 +1.37 % + Run_MD_PW md_ions_pw +63.66 1 +63.66 +93.06 % + Electrons self_consistent +54.24 3 +18.08 +79.30 % + Electrons c_bands +26.27 30 +0.88 +38.41 % + Hamilt diagH_pw +26.15 30 +0.87 +38.23 % + Diago_CG diag +23.65 32 +0.74 +34.57 % + Charge sum_band +2.40 30 +0.08 +3.50 % + Charge rho_mpi +0.91 30 +0.03 +1.33 % + Charge mix_rho +0.81 30 +0.03 +1.18 % + Forces cal_force_nl +0.22 3 +0.07 +0.33 % + Stress_PW cal_stress +3.14 3 +1.05 +4.59 % + Stress_Func stress_ew +20.85 2 +10.42 +30.48 % + Force_Func stress_ew +20.85 2 +10.42 +30.48 % + Stress_Func stress_gga +0.12 3 +0.04 +0.17 % + Stress_Func stress_loc +1.30 3 +0.43 +1.91 % + Stress_Func stres_nl +1.62 3 +0.54 +2.36 % + ---------------------------------------------------------------------------------------- + + CLASS_NAME---------|NAME---------------|MEMORY(MB)-------- + +64.7285 + Charge_Pulay Rrho +11.8652 + Charge_Pulay dRrho +10.3821 + Charge_Pulay drho +10.3821 + Use_FFT porter +2.9663 + PW_Basis struc_fac +2.5229 + wavefunc evc +2.2076 + Charge rho +1.4832 + Charge rho_save +1.4832 + Charge rho_core +1.4832 + Potential vltot +1.4832 + Potential vr +1.4832 + Potential vr_eff +1.4832 + Potential vr_eff1 +1.4832 + Potential vnew +1.4832 + Charge_Pulay rho_save2 +1.4832 + ---------------------------------------------------------- + + Start Time : Fri Nov 12 18:17:38 2021 + Finish Time : Fri Nov 12 18:18:46 2021 + Total Time : 0 h 1 mins 8 secs diff --git a/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/STRU b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/STRU new file mode 100644 index 000000000..8bc79faf7 --- /dev/null +++ b/tests/data/out_data_02_md_abacus/02.md/sys-0004-0001/scale-0.950/000002/STRU @@ -0,0 +1,25 @@ +ATOMIC_SPECIES +H 1.008 H_ONCV_PBE-1.0.upf +C 12.010 C_ONCV_PBE-1.0.upf + +LATTICE_CONSTANT +1.8897261254578281 + +LATTICE_VECTORS +9.270692584805424 0.0 0.0 +0.01282384569524753 9.562095202737858 0.0 +0.16956077473517553 -0.030030528263640357 9.586097955682344 + +ATOMIC_POSITIONS +Cartesian # Cartesian(Unit is LATTICE_CONSTANT) +H +0.0 +4 +5.092906051636 3.892428715541 3.458357779363 1 1 1 +3.803610942086 4.550057118756 4.167057547630 1 1 1 +5.219812881472 5.333210396361 4.208595102670 1 1 1 +5.008148307232 3.980023448407 5.084711945455 1 1 1 +C +0.0 +1 +4.787734579020 4.439473905493 4.223441759937 1 1 1 diff --git a/tests/data/test_coll_abacus.py b/tests/data/test_coll_abacus.py new file mode 100644 index 000000000..6a73b7233 --- /dev/null +++ b/tests/data/test_coll_abacus.py @@ -0,0 +1,63 @@ +import os,sys,json,glob,shutil +import dpdata +import numpy as np +import unittest + +sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) +__package__ = 'data' +from .context import coll_abacus_md +from .context import out_dir_name +from .context import abacus_param_file +from .context import setUpModule + +class TestCollAbacus(unittest.TestCase): + def setUp(self): + with open (abacus_param_file, 'r') as fp : + jdata = json.load (fp) + self.odir = out_dir_name(jdata) + assert os.path.isdir('out_data_02_md_abacus'), 'out data for post fp vasp should exist' + if os.path.isdir(self.odir) : + shutil.rmtree(self.odir) + shutil.copytree('out_data_02_md_abacus', self.odir) + self.ref_coord = np.reshape(np.genfromtxt("abacus.out/coord.raw"), [9, 5, 3]) + self.ref_cell = np.reshape(np.genfromtxt("abacus.out/box.raw"), [9, 3, 3]) + self.ref_e = np.reshape(np.genfromtxt("abacus.out/energy.raw"), [9, ]) + self.ref_f = np.reshape(np.genfromtxt("abacus.out/force.raw"), [9, 5, 3]) + self.ref_v = np.reshape(np.genfromtxt("abacus.out/virial.raw"), [9, 3, 3]) + def tearDown(self): + #print("escape.") + shutil.rmtree(self.odir) + + def test_coll(self): + + with open (abacus_param_file, 'r') as fp : + jdata = json.load (fp) + jdata['out_dir'] = self.odir + print(os.getcwd()) + coll_abacus_md(jdata) + + sys = dpdata.LabeledSystem(self.odir + '/02.md/sys-0004-0001/deepmd//', fmt = 'deepmd/raw') + self.assertEqual(sys.get_nframes(), 9) + + for ff in range(9) : + self.assertAlmostEqual(self.ref_e[ff], sys.data['energies'][ff]) + for ff in range(9) : + for ii in range(5) : + for dd in range(3) : + self.assertAlmostEqual(self.ref_coord[ff][ii][dd], + sys.data['coords'][ff][ii][dd]) + self.assertAlmostEqual(self.ref_f[ff][ii][dd], + sys.data['forces'][ff][ii][dd]) + for ff in range(9): + for ii in range(3) : + for jj in range(3) : + self.assertAlmostEqual(self.ref_v[ff][ii][jj], + sys.data['virials'][ff][ii][jj], places = 5) + self.assertAlmostEqual(self.ref_cell[ff][ii][jj], + sys.data['cells'][ff][ii][jj]) + +if __name__ == '__main__': + unittest.main() + + + diff --git a/tests/data/test_coll_vasp.py b/tests/data/test_coll_vasp.py index 716e67163..b13f99403 100644 --- a/tests/data/test_coll_vasp.py +++ b/tests/data/test_coll_vasp.py @@ -84,6 +84,8 @@ def test_coll(self): self.assertAlmostEqual(ref_cell[ff][ii][jj], sys.data['cells'][ff][ii][jj]) +if __name__ == '__main__': + unittest.main() diff --git a/tests/data/test_gen_bulk.py b/tests/data/test_gen_bulk.py index 73572d4e8..54a9cfd61 100644 --- a/tests/data/test_gen_bulk.py +++ b/tests/data/test_gen_bulk.py @@ -12,6 +12,8 @@ def setUp(self): self.alloy=[] with open (param_file, 'r') as fp : jdata = json.load (fp) + if "init_fp_style" not in jdata: + jdata["init_fp_style"] = "VASP" out_dir = out_dir_name(jdata) self.out_dir= out_dir jdata['out_dir'] = out_dir @@ -52,3 +54,7 @@ def test(self): for scale in scales: perts=glob.glob(os.path.join(scale,"[0-9]*")) self.assertEqual(len(perts),self.pert_numb+1) + + +if __name__ == '__main__': + unittest.main() \ No newline at end of file diff --git a/tests/data/test_gen_bulk_abacus.py b/tests/data/test_gen_bulk_abacus.py new file mode 100644 index 000000000..4ac7ef39f --- /dev/null +++ b/tests/data/test_gen_bulk_abacus.py @@ -0,0 +1,55 @@ +import os,sys,json,glob,shutil +import unittest + +sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))) +__package__ = 'data' +from .context import setUpModule +from .context_bulk import * + +class TestGenBulkABACUS(unittest.TestCase): + def setUp(self): + self.alloy=[] + with open (abacus_param_file, 'r') as fp : + jdata = json.load (fp) + out_dir = out_dir_name(jdata) + self.out_dir= out_dir + jdata['out_dir'] = out_dir + self.elements=jdata["elements"] + self.scale_numb=len(jdata["scale"]) + self.pert_numb=jdata["pert_numb"] + self.root_dir= out_dir + create_path(out_dir) + stru_data = make_unit_cell_ABACUS(jdata) + supercell_stru = make_super_cell_ABACUS(jdata, stru_data) + place_element_ABACUS(jdata, supercell_stru) + make_abacus_relax(jdata, {"fp_resources":{}}) + make_scale_ABACUS(jdata) + pert_scaled(jdata) + + def tearDown(self): + shutil.rmtree(self.root_dir) + + def test(self): + path=self.out_dir+"/00.place_ele" + #struct0=Structure.from_file(os.path.join(path,"STRU")) + alloys=glob.glob(os.path.join(path,"sys-*")) + stru0 = get_abacus_STRU(os.path.join(alloys[0], "STRU")) + self.assertEqual(len(alloys),stru0['coords'].shape[0]-1) + for ii in alloys: + elem_numb=[int(i) for i in ii.split('/')[-1].split('-')[1:]] + struct=get_abacus_STRU(os.path.join(ii,"STRU")) + self.assertEqual(struct["atom_names"],self.elements) + self.assertEqual(struct["atom_numbs"], elem_numb) + path=self.out_dir+"/01.scale_pert" + alloys=glob.glob(os.path.join(path,"sys-*")) + self.assertEqual(len(alloys), stru0['coords'].shape[0]-1) + for ii in alloys: + scales=glob.glob(os.path.join(ii,"scale-*")) + self.assertEqual(len(scales),self.scale_numb) + for scale in scales: + perts=glob.glob(os.path.join(scale,"[0-9]*")) + self.assertEqual(len(perts),self.pert_numb+1) + + +if __name__ == '__main__': + unittest.main() \ No newline at end of file diff --git a/tests/generator/out_data_post_fp_cp2k/orig/box.raw b/tests/generator/out_data_post_fp_cp2k/orig/box.raw index 7de7fc209..ba9babfb2 100644 --- a/tests/generator/out_data_post_fp_cp2k/orig/box.raw +++ b/tests/generator/out_data_post_fp_cp2k/orig/box.raw @@ -1 +1 @@ -1.080400000000000027e+01 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.049799999999999933e+01 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.095599999999999952e+01 +1.080399990081787109e+01 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.049800014495849609e+01 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 1.095600032806396484e+01 diff --git a/tests/generator/out_data_post_fp_cp2k/orig/coord.raw b/tests/generator/out_data_post_fp_cp2k/orig/coord.raw index f95b14882..fbad9852a 100644 --- a/tests/generator/out_data_post_fp_cp2k/orig/coord.raw +++ b/tests/generator/out_data_post_fp_cp2k/orig/coord.raw @@ -1 +1 @@ -1.027355000000000018e+00 1.706661999999999901e+00 1.602476000000000012e+00 3.963681999999999928e+00 3.976694999999999869e+00 3.215037000000000145e+00 4.365914000000000073e+00 5.882829000000000086e+00 5.464286000000000421e+00 1.528405999999999931e+00 2.262055000000000149e+00 3.791755000000000209e+00 6.766289000000000442e+00 7.323279000000000316e+00 7.395023000000000124e+00 8.059174999999999756e+00 9.176418999999999215e+00 5.758306000000000147e+00 +1.027354955673217773e+00 1.706662058830261230e+00 1.602476000785827637e+00 3.963681936264038086e+00 3.976695060729980469e+00 3.215037107467651367e+00 4.365913867950439453e+00 5.882829189300537109e+00 5.464285850524902344e+00 1.528406023979187012e+00 2.262054920196533203e+00 3.791754961013793945e+00 6.766289234161376953e+00 7.323278903961181641e+00 7.395022869110107422e+00 8.059174537658691406e+00 9.176419258117675781e+00 5.758306026458740234e+00 diff --git a/tests/generator/out_data_post_fp_cp2k/orig/energy.raw b/tests/generator/out_data_post_fp_cp2k/orig/energy.raw index 362e9a65e..16e1e92a4 100644 --- a/tests/generator/out_data_post_fp_cp2k/orig/energy.raw +++ b/tests/generator/out_data_post_fp_cp2k/orig/energy.raw @@ -1 +1 @@ --8.447582606992446017e+02 +-8.447582397460937500e+02 diff --git a/tests/generator/out_data_post_fp_cp2k/orig/force.raw b/tests/generator/out_data_post_fp_cp2k/orig/force.raw index 0ad41126e..eb099f7db 100644 --- a/tests/generator/out_data_post_fp_cp2k/orig/force.raw +++ b/tests/generator/out_data_post_fp_cp2k/orig/force.raw @@ -1 +1 @@ -6.917656471387700901e-01 7.553510904559461725e-01 2.274964715661485837e+00 -3.209683176564304130e-01 2.775192417423087421e-01 9.094059481875964579e-01 -6.332576187642065257e-02 -6.449617955424929994e-01 -8.145296625904011600e-01 -1.756151021831240944e-01 -3.121818289867506202e-01 -2.260577849622959601e+00 1.112470664210258198e+00 1.688659044047888358e+00 -1.721519802047959624e+00 -1.208800137434334454e+00 -1.778025455114995435e+00 1.601097547549200639e+00 +6.917656660079956055e-01 7.553510665893554688e-01 2.274964809417724609e+00 -3.209683299064636230e-01 2.775192558765411377e-01 9.094060063362121582e-01 -6.332576274871826172e-02 -6.449618339538574219e-01 -8.145296573638916016e-01 -1.756150871515274048e-01 -3.121818304061889648e-01 -2.260577917098999023e+00 1.112470626831054688e+00 1.688659071922302246e+00 -1.721519827842712402e+00 -1.208800196647644043e+00 -1.778025507926940918e+00 1.601097583770751953e+00