Merge pull request #200 from deepmodeling/devel

merge devel to master

.travis.yml

@@ -1,12 +1,10 @@
 language: python
 python:
-  - "3.6.3"
-  - "3.6-dev"  # 3.6 development branch
+  - "3.6"
+  - "3.7"
 # command to install dependencies
 env:
   matrix:
-  - PYMATGEN_VERSION=2017.9.1
-  - PYMATGEN_VERSION=2018.1.19
   - PYMATGEN_VERSION=2019.1.13
   - PYMATGEN_VERSION=2019.7.30
 before_install:

dpgen/auto_test/cmpt_00_equi.py

@@ -21,48 +21,43 @@ def comput_e_shift(poscar, task_name) :
             ener_shift += a_natoms[ii] * ener
     return ener_shift
 
-def comput_lmp_nev(conf_dir, task_name, write_stable = False) :
+def comput_lmp_nev(conf_dir, task_name,write_shift = False) :
     conf_path = re.sub('confs', global_equi_name, conf_dir)
     conf_path = os.path.abspath(conf_path)
     poscar = os.path.join(conf_path, 'POSCAR')
-    if write_stable :
-        ele_types = vasp.get_poscar_types(poscar) 
-        if len(ele_types) > 1 :
-            raise RuntimeError('stable energy and volume only for one element, current you have %s from POSCAR' % str(ele_types))
-    ener_shift = comput_e_shift(poscar, task_name)
+    ele_types = vasp.get_poscar_types(poscar)
 
     lmp_path = os.path.join(conf_path, task_name)
     log_lammps = os.path.join(lmp_path, 'log.lammps')
     if os.path.isfile(log_lammps):
         natoms, epa, vpa = lammps.get_nev(log_lammps)
-        epa = (epa * natoms - ener_shift) / natoms
-        if write_stable :
+        if write_shift and len(ele_types)>1:
+            ener_shift = comput_e_shift(poscar, task_name)
+            shift = (epa * natoms - ener_shift) / natoms
+            return natoms,epa,vpa,shift
+        if len(ele_types)==1:
             stable_dir = 'stables'
             os.makedirs(stable_dir, exist_ok=True)
             name_prefix=os.path.join(stable_dir,'%s.%s' % (ele_types[0], task_name))
             open(name_prefix + '.e', 'w').write('%.16f\n' % (epa))
             open(name_prefix + '.v', 'w').write('%.16f\n' % (vpa))
-        return natoms, epa, vpa
+        return natoms, epa, vpa , None
     else :
-        return None, None, None
+        return None, None, None, None
+
+def comput_vasp_nev(jdata, conf_dir, write_shift = False) :
 
-def comput_vasp_nev(jdata, conf_dir, write_stable = False) :
-
     conf_path = re.sub('confs', global_equi_name, conf_dir)
     conf_path = os.path.abspath(conf_path)
     poscar = os.path.join(conf_path, 'POSCAR')
-    if write_stable :
-        ele_types = vasp.get_poscar_types(poscar) 
-        if len(ele_types) > 1 :
-            raise RuntimeError('stable energy and volume only for one element, current you have %s from POSCAR' % str(ele_types))
+    ele_types = vasp.get_poscar_types(poscar)
 
     if 'relax_incar' in jdata.keys():
         vasp_str='vasp-relax_incar'
     else:
         kspacing = jdata['vasp_params']['kspacing']
         vasp_str='vasp-k%.2f' % kspacing
 
-    ener_shift = comput_e_shift(poscar, vasp_str)
     vasp_path = os.path.join(conf_path, vasp_str)
     outcar = os.path.join(vasp_path, 'OUTCAR')
     # tag_fin = os.path.join(vasp_path, 'tag_finished')
@@ -72,22 +67,25 @@ def comput_vasp_nev(jdata, conf_dir, write_stable = False) :
         warnings.warn("incomplete job "+vasp_path+" use the last frame")
     if os.path.isfile(outcar):
         natoms, epa, vpa = vasp.get_nev(outcar)
-        epa = (epa * natoms - ener_shift) / natoms
-        if write_stable :
+        if write_shift and len(ele_types)>1:
+            ener_shift = comput_e_shift(poscar, vasp_str)
+            shift = (epa * natoms - ener_shift) / natoms
+            return natoms,epa,vpa,shift
+        if len(ele_types)==1:
             stable_dir = 'stables'
             os.makedirs(stable_dir, exist_ok=True)
             name_prefix=os.path.join(stable_dir,'%s.'% (ele_types[0])+vasp_str)
             open(name_prefix + '.e', 'w').write('%.16f\n' % (epa))
             open(name_prefix + '.v', 'w').write('%.16f\n' % (vpa))
-        return natoms, epa, vpa
+        return natoms, epa, vpa, None
     else :
-        return None, None, None
+        return None, None, None, None
 
 def _main():
     parser = argparse.ArgumentParser(
         description="cmpt 00.equi")
-    parser.add_argument('TASK', type=str, 
-                        choices = ['all', 'vasp', 'deepmd', 'meam'], 
+    parser.add_argument('TASK', type=str,
+                        choices = ['all', 'vasp', 'deepmd', 'meam'],
                         help='the task of generation, vasp or lammps')
     parser.add_argument('PARAM', type=str,
                         help='the json param')
@@ -120,4 +118,3 @@ def _main():
 
 if __name__ == '__main__' :
     _main()
-

dpgen/auto_test/cmpt_02_elastic.py

@@ -104,7 +104,7 @@ def cmpt_deepmd_lammps(jdata, conf_dir, task_name) :
     # et = -et / 1e4
     print_et(et)
     result = os.path.join(task_path,'result')
-    result_et(et,conf_dir,task_path)
+    result_et(et,conf_dir,result)
     if 'upload_username' in jdata.keys() and task_name=='deepmd':
         upload_username=jdata['upload_username']
         util.insert_data('elastic','deepmd',upload_username,result)

dpgen/auto_test/cmpt_03_vacancy.py

@@ -23,7 +23,7 @@ def comput_e_shift(poscar, task_name) :
         ref_e_file = os.path.join('stables', ref_e_file)
         ener = float(open(ref_e_file).read())
         ener_shift += a_natoms[ii] * ener
-    return ener_shift 
+    return ener_shift
 
 def cmpt_vasp(jdata, conf_dir, supercell) :
 
@@ -37,7 +37,7 @@ def cmpt_vasp(jdata, conf_dir, supercell) :
     equi_path = os.path.join(equi_path, vasp_str)
     equi_path = os.path.abspath(equi_path)
     equi_outcar = os.path.join(equi_path, 'OUTCAR')
-    task_path = re.sub('confs', global_task_name, conf_dir)    
+    task_path = re.sub('confs', global_task_name, conf_dir)
     task_path = os.path.join(task_path, vasp_str)
     task_path = os.path.abspath(task_path)
     print("# ", task_path)
@@ -51,17 +51,23 @@ def cmpt_vasp(jdata, conf_dir, supercell) :
     if len(struct_path_list) == 0:
         print("# cannot find results for conf %s supercell %s" % (conf_dir, supercell))
     sys.stdout.write ("Structure: \tVac_E(eV)  E(eV) equi_E(eV)\n")
-    for ii in struct_path_list :
-        struct_poscar = os.path.join(ii, 'POSCAR')
-        energy_shift = comput_e_shift(struct_poscar, vasp_str)
-        structure_dir = os.path.basename(ii)
-        outcar = os.path.join(ii, 'OUTCAR')
-        natoms, epa, vpa = vasp.get_nev(outcar)
-        evac = epa * natoms - equi_epa * natoms
-        sys.stdout.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa*natoms))
+    result = os.path.join(task_path,'result')
+    with open(result,'w') as fp:
+        fp.write('conf_dir:%s\n'% (conf_dir))
+        fp.write("Structure: \tVac_E(eV)  E(eV) equi_E(eV)\n")
+        for ii in struct_path_list :
+            struct_poscar = os.path.join(ii, 'POSCAR')
+            #energy_shift = comput_e_shift(struct_poscar, vasp_str)
+            structure_dir = os.path.basename(ii)
+            outcar = os.path.join(ii, 'OUTCAR')
+            natoms, epa, vpa = vasp.get_nev(outcar)
+            evac = epa * natoms - equi_epa * natoms
+            sys.stdout.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa*natoms))
+            fp.write("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa*natoms))
+    fp.close()
         # evac = epa * natoms - energy_shift
         # sys.stdout.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, energy_shift))
-        # sys.stdout.write ("%s: %7.3f \n" % (structure_dir, evac))    
+        # sys.stdout.write ("%s: %7.3f \n" % (structure_dir, evac))
 
 def cmpt_deepmd_lammps(jdata, conf_dir, supercell, task_name) :
     equi_path = re.sub('confs', global_equi_name, conf_dir)
@@ -82,14 +88,20 @@ def cmpt_deepmd_lammps(jdata, conf_dir, supercell, task_name) :
     if len(struct_path_list) == 0:
         print("# cannot find results for conf %s supercell %s" % (conf_dir, supercell))
     sys.stdout.write ("Structure: \tVac_E(eV)  E(eV) equi_E(eV)\n")
-    for ii in struct_path_list :
-        struct_poscar = os.path.join(ii, 'POSCAR')
-        energy_shift = comput_e_shift(struct_poscar, task_name)
-        structure_dir = os.path.basename(ii)
-        lmp_log = os.path.join(ii, 'log.lammps')
-        natoms, epa, vpa = lammps.get_nev(lmp_log)
-        evac = epa * natoms - equi_epa * natoms
-        sys.stdout.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa * natoms))
+    result = os.path.join(task_path,'result')
+    with open(result,'w') as fp:
+        fp.write('conf_dir:%s\n'% (conf_dir))
+        fp.write("Structure: \tVac_E(eV)  E(eV) equi_E(eV)\n")
+        for ii in struct_path_list :
+            struct_poscar = os.path.join(ii, 'POSCAR')
+            #energy_shift = comput_e_shift(struct_poscar, task_name)
+            structure_dir = os.path.basename(ii)
+            lmp_log = os.path.join(ii, 'log.lammps')
+            natoms, epa, vpa = lammps.get_nev(lmp_log)
+            evac = epa * natoms - equi_epa * natoms
+            sys.stdout.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa * natoms))
+            fp.write("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa*natoms))
+    fp.close()
         # evac = epa * natoms - energy_shift
         # sys.stdout.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, energy_shift))
         # sys.stdout.write ("%s: %7.3f\n" % (structure_dir, evac))
@@ -112,15 +124,13 @@ def _main() :
 
 #    print('# generate %s task with conf %s' % (args.TASK, args.CONF))
     if args.TASK == 'vasp':
-        cmpt_vasp(jdata, args.CONF, args.COPY)               
+        cmpt_vasp(jdata, args.CONF, args.COPY)
     elif args.TASK == 'deepmd' :
         cmpt_deepmd_lammps(jdata, args.CONF, args.COPY, args.TASK)
     elif args.TASK == 'meam' :
         cmpt_deepmd_lammps(jdata, args.CONF, args.COPY, args.TASK)
     else :
         raise RuntimeError("unknow task ", args.TASK)
-    
+
 if __name__ == '__main__' :
     _main()
-
-

dpgen/auto_test/cmpt_04_interstitial.py

@@ -41,13 +41,19 @@ def _cmpt_vasp(jdata, conf_dir, supercell, insert_ele) :
     struct_path_list.sort()
     if len(struct_path_list) == 0:
         print("# cannot find results for conf %s supercell %s" % (conf_dir, supercell))
-    sys.stdout.write ("Insert_ele-Struct: Inter_E(eV)\n")
-    for ii in struct_path_list :
-        structure_dir = os.path.basename(ii)
-        outcar = os.path.join(ii, 'OUTCAR')
-        natoms, epa, vpa = vasp.get_nev(outcar)
-        evac = epa * natoms - equi_epa * natoms
-        sys.stdout.write ("%s: %7.3f \n" % (structure_dir, evac))    
+    sys.stdout.write ("Insert_ele-Struct: Inter_E(eV)  E(eV) equi_E(eV)\n")
+    result = os.path.join(task_path,'result')
+    with open(result,'w') as fp:
+        fp.write('conf_dir:%s\n'% (conf_dir))
+        fp.write ("Insert_ele-Struct: Inter_E(eV)  E(eV) equi_E(eV)\n")
+        for ii in struct_path_list :
+            structure_dir = os.path.basename(ii)
+            outcar = os.path.join(ii, 'OUTCAR')
+            natoms, epa, vpa = vasp.get_nev(outcar)
+            evac = epa * natoms - equi_epa * natoms
+            sys.stdout.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa * natoms))
+            fp.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa * natoms))
+    fp.close()
 
 def cmpt_deepmd_reprod_traj(jdata, conf_dir, supercell, insert_ele, task_name) :
     for ii in insert_ele:
@@ -63,7 +69,7 @@ def _cmpt_deepmd_reprod_traj(jdata, conf_dir, supercell, insert_ele, task_name)
     conf_path = os.path.abspath(conf_dir)
     task_path = re.sub('confs', global_task_name, conf_path)
     vasp_path = os.path.join(task_path, vasp_str)
-    lmps_path = os.path.join(task_path, task_name + vasp_str.replace('vasp',''))    
+    lmps_path = os.path.join(task_path, task_name + vasp_str.replace('vasp',''))
     copy_str = "%sx%sx%s" % (supercell[0], supercell[1], supercell[2])
     struct_widecard = os.path.join(vasp_path, 'struct-%s-%s-*' % (insert_ele,copy_str))
     vasp_struct = glob.glob(struct_widecard)
@@ -122,12 +128,18 @@ def _cmpt_deepmd_lammps(jdata, conf_dir, supercell, insert_ele, task_name) :
     if len(struct_path_list) == 0:
         print("# cannot find results for conf %s supercell %s" % (conf_dir, supercell))
     sys.stdout.write ("Insert_ele-Struct: Inter_E(eV)  E(eV) equi_E(eV)\n")
-    for ii in struct_path_list :
-        structure_dir = os.path.basename(ii)
-        lmp_log = os.path.join(ii, 'log.lammps')
-        natoms, epa, vpa = lammps.get_nev(lmp_log)
-        evac = epa * natoms - equi_epa * natoms
-        sys.stdout.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa * natoms))
+    result = os.path.join(task_path,'result')
+    with open(result,'w') as fp:
+        fp.write('conf_dir:%s\n'% (conf_dir))
+        fp.write ("Insert_ele-Struct: Inter_E(eV)  E(eV) equi_E(eV)\n")
+        for ii in struct_path_list :
+            structure_dir = os.path.basename(ii)
+            lmp_log = os.path.join(ii, 'log.lammps')
+            natoms, epa, vpa = lammps.get_nev(lmp_log)
+            evac = epa * natoms - equi_epa * natoms
+            sys.stdout.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa * natoms))
+            fp.write ("%s: %7.3f  %7.3f %7.3f \n" % (structure_dir, evac, epa * natoms, equi_epa * natoms))
+    fp.close()
 
 def _main() :
     parser = argparse.ArgumentParser(
@@ -149,7 +161,7 @@ def _main() :
 
 #    print('# generate %s task with conf %s' % (args.TASK, args.CONF))
     if args.TASK == 'vasp':
-        cmpt_vasp(jdata, args.CONF, args.COPY, args.ELEMENT)               
+        cmpt_vasp(jdata, args.CONF, args.COPY, args.ELEMENT)
     elif args.TASK == 'deepmd' :
         cmpt_deepmd_lammps(jdata, args.CONF, args.COPY, args.ELEMENT, args.TASK)
     elif args.TASK == 'deepmd-reprod' :
@@ -160,8 +172,6 @@ def _main() :
         cmpt_deepmd_reprod_traj(jdata, args.CONF, args.COPY, args.ELEMENT, args.TASK)
     else :
         raise RuntimeError("unknow task ", args.TASK)
-    
+
 if __name__ == '__main__' :
     _main()
-
-

dpgen/auto_test/cmpt_05_surf.py

@@ -96,7 +96,7 @@ def cmpt_deepmd_lammps(jdata, conf_dir, task_name, static = False) :
             sys.stdout.write ("%s: \t%7.3f    %8.3f %8.3f\n" % (structure_dir, evac, epa, equi_epa))
             fp.write("%s:\t %7.3f   %8.3f %8.3f\n" % (structure_dir, evac, epa, equi_epa))
     fp.close()
-    if 'upload_username' in jdata.keys() and task_name=='deepm':
+    if 'upload_username' in jdata.keys() and task_name=='deepmd':
         upload_username=jdata['upload_username']
         util.insert_data('surf','deepmd',upload_username,result)