Merge pull request #5 from nanotech-empa/release/1.4.2

Release/1.4.2
nanotech-empa · Apr 30, 2021 · a150879 · a150879
2 parents b4ff37e + 27e11b0
commit a150879
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Showing 4 changed files with 26 additions and 19 deletions.
diff --git a/common.py b/common.py
@@ -22,23 +22,24 @@
 ### BS & PP
 
 ATOMIC_KIND_INFO = {
-    'H' :{'basis' : 'TZV2P-MOLOPT-GTH'  , 'pseudo' : 'GTH-PBE-q1' },
-    'Au':{'basis' : 'DZVP-MOLOPT-SR-GTH', 'pseudo' : 'GTH-PBE-q11'},
-    'Ag':{'basis' : 'DZVP-MOLOPT-SR-GTH', 'pseudo' : 'GTH-PBE-q11'},
-    'Cu':{'basis' : 'DZVP-MOLOPT-SR-GTH', 'pseudo' : 'GTH-PBE-q11'},
-    'Al':{'basis' : 'DZVP-MOLOPT-SR-GTH', 'pseudo' : 'GTH-PBE-q3' },
-    'B' :{'basis' : 'DZVP-MOLOPT-SR-GTH', 'pseudo' : 'GTH-PBE-q3' },
-    'Br':{'basis' : 'DZVP-MOLOPT-SR-GTH', 'pseudo' : 'GTH-PBE-q7' },
-    'C' :{'basis' : 'TZV2P-MOLOPT-GTH'  , 'pseudo' : 'GTH-PBE-q4' },
-    'Si':{'basis' : 'DZVP-MOLOPT-GTH'   , 'pseudo' : 'GTH-PBE-q4' },
-    'Ga':{'basis' : 'DZVP-MOLOPT-SR-GTH', 'pseudo' : 'GTH-PBE-q13'},
-    'N' :{'basis' : 'TZV2P-MOLOPT-GTH'  , 'pseudo' : 'GTH-PBE-q5' },
-    'O' :{'basis' : 'TZV2P-MOLOPT-GTH'  , 'pseudo' : 'GTH-PBE-q6' },
-    'Pd':{'basis' : 'DZVP-MOLOPT-SR-GTH', 'pseudo' : 'GTH-PBE-q18'},
-    'S' :{'basis' : 'TZV2P-MOLOPT-GTH'  , 'pseudo' : 'GTH-PBE-q6' },
-    'Zn':{'basis' : 'DZVP-MOLOPT-SR-GTH', 'pseudo' : 'GTH-PBE-q12'},
+    'H' :{'basis' : 'TZV2P-MOLOPT-GTH'   , 'pseudo' : 'GTH-PBE-q1'   }, #1
+    'B' :{'basis' : 'DZVP-MOLOPT-SR-GTH' , 'pseudo' : 'GTH-PBE-q3'   }, #5
+    'C' :{'basis' : 'TZV2P-MOLOPT-GTH'   , 'pseudo' : 'GTH-PBE-q4'   }, #6
+    'N' :{'basis' : 'TZV2P-MOLOPT-GTH'   , 'pseudo' : 'GTH-PBE-q5'   }, #7
+    'O' :{'basis' : 'TZV2P-MOLOPT-GTH'   , 'pseudo' : 'GTH-PBE-q6'   }, #8
+    'Al':{'basis' : 'DZVP-MOLOPT-SR-GTH' , 'pseudo' : 'GTH-PBE-q3'   }, #13
+    'Si':{'basis' : 'DZVP-MOLOPT-GTH'    , 'pseudo' : 'GTH-PBE-q4'   }, #14
+    'S' :{'basis' : 'TZV2P-MOLOPT-GTH'   , 'pseudo' : 'GTH-PBE-q6'   }, #16
+    'Cl':{'basis' : 'TZV2P-MOLOPT-GTH'   , 'pseudo' : 'GTH-PBE-q7'   }, #17
+    'Cu':{'basis' : 'DZVP-MOLOPT-SR-GTH' , 'pseudo' : 'GTH-PBE-q11'  }, #29
+    'Zn':{'basis' : 'DZVP-MOLOPT-SR-GTH' , 'pseudo' : 'GTH-PBE-q12'  }, #30
+    'Ga':{'basis' : 'DZVP-MOLOPT-SR-GTH' , 'pseudo' : 'GTH-PBE-q13'  }, #31
+    'Br':{'basis' : 'DZVP-MOLOPT-SR-GTH' , 'pseudo' : 'GTH-PBE-q7'   }, #35
+    'Pd':{'basis' : 'DZVP-MOLOPT-SR-GTH' , 'pseudo' : 'GTH-PBE-q18'  }, #46
+    'Ag':{'basis' : 'DZVP-MOLOPT-SR-GTH' , 'pseudo' : 'GTH-PBE-q11'  }, #47
+    'Au':{'basis' : 'DZVP-MOLOPT-SR-GTH' , 'pseudo' : 'GTH-PBE-q11'  }, #79 
 }
-
+    
 ### ----------------------------------------------------------------
 ### ----------------------------------------------------------------
 ### ----------------------------------------------------------------

diff --git a/metadata.json b/metadata.json
@@ -1,7 +1,7 @@
 {
     "description": "App to run scanning probe microscopy simulations.",
     "title": "Empa nanotech@surfaces Laboratory - Scanning Probe Microscopy",
-    "version": "1.4.1",
+    "version": "1.4.2",
     "logo": "miscellaneous/logos/empa.png",
     "authors": "nanotech@surfaces laboratory, Empa",
     "state": "stable"

diff --git a/orb/submit_orb.ipynb b/orb/submit_orb.ipynb
@@ -345,6 +345,9 @@
     "        dft_params = Dict(dict=dft_params_dict)\n",
     "\n",
     "        extrap_plane = extrap_plane_floattext.value\n",
+    "        max_height = max([float(h) for h in heights_text.value.split()])\n",
+    "        extrap_extent = max([max_height - extrap_plane, 5.0])\n",
+    "        \n",
     "        parent_dir = \"parent_calc_folder/\"\n",
     "        stm_params = Dict(dict={\n",
     "            '--cp2k_input_file':    parent_dir+'aiida.inp',\n",
@@ -356,7 +359,7 @@
     "            '--eval_region':        ['G', 'G', 'G', 'G', 'n-1.0_C', 'p%.1f'%extrap_plane],\n",
     "            '--dx':                 '0.15',\n",
     "            '--eval_cutoff':        '14.0',\n",
-    "            '--extrap_extent':      '5.0',\n",
+    "            '--extrap_extent':      str(extrap_extent),\n",
     "            '--n_homo':             str(n_homo_inttext.value+2),\n",
     "            '--n_lumo':             str(n_lumo_inttext.value+2),\n",
     "            '--orb_heights':        heights_text.value.split(),\n",

diff --git a/stm/submit_stm.ipynb b/stm/submit_stm.ipynb
@@ -285,6 +285,9 @@
     "        \n",
     "        \n",
     "        extrap_plane = extrap_plane_floattext.value\n",
+    "        max_height = max([float(h) for h in const_height_text.value.split()])\n",
+    "        extrap_extent = max([max_height - extrap_plane, 5.0])\n",
+    "        \n",
     "        parent_dir = \"parent_calc_folder/\"\n",
     "        \n",
     "        energy_range_str = \"%.2f %.2f %.3f\" % (\n",
@@ -301,7 +304,7 @@
     "            '--eval_region':        ['G', 'G', 'G', 'G', 'n-2.0_C', 'p%.1f'%extrap_plane],\n",
     "            '--dx':                 '0.15',\n",
     "            '--eval_cutoff':        '14.0',\n",
-    "            '--extrap_extent':      '5.0',\n",
+    "            '--extrap_extent':      str(extrap_extent),\n",
     "            '--energy_range':       energy_range_str.split(),\n",
     "            '--heights':            const_height_text.value.split(),\n",
     "            '--isovalues':          const_current_text.value.split(),\n",