Merge branch 'master' into 'release'

Release of Amolqc Version 7.1.0 (Helium)

See merge request luechow-group/Amolqc!12

.zenodo.json

@@ -0,0 +1,73 @@
+{
+  "title": "Amolqc",
+  "description": "<p><strong>Atoms and Molecules with Quantum Monte Carlo</strong></p>",
+  "license": "GPL-3.0-or-later",
+  "creators": [
+    {
+      "orcid": "0000-0002-1068-0674",
+      "affiliation": "RWTH Aachen University",
+      "name": "Lüchow, Arne"
+    },
+    {
+      "name": "Manten, Sebastian"
+    },
+    {
+      "name": "Diedrich, Christian"
+    },
+    {
+      "orcid": "0000-0003-3827-9169",
+      "name": "Bande, Annika"
+    },
+    {
+      "name": "Scott, Tony C."
+    },
+    {
+      "name": "Schwarz, Annett"
+    },
+    {
+      "name": "Berner, Raphael"
+    },
+    {
+      "name": "Petz, Rene"
+    },
+    {
+      "name": "Sturm, Alexander"
+    },
+    {
+      "name": "Hermsen,Marko"
+    },
+    {
+      "orcid": "0000-0002-8578-4961",
+      "affiliation": "RWTH Aachen University",
+      "name": "Mood, Kaveh Haghighi"
+    },
+    {
+      "affiliation": "RWTH Aachen University",
+      "name": "Schulte, Christoph"
+    },
+    {
+      "orcid": "0000-0001-5758-843X",
+      "affiliation": "RWTH Aachen University",
+      "name": "Reuter, Leonard"
+    },
+    {
+      "orcid": "0000-0003-2113-6129",
+      "affiliation": "RWTH Aachen University",
+      "name": "Heuer, Michael A."
+    },
+    {
+      "orcid": "0000-0002-4144-2089",
+      "affiliation": "RWTH Aachen University",
+      "name": "Ludovicy, Jil"
+    }
+  ],
+  "keywords": [
+    "quantum chemistry",
+    "variational Monte Carlo",
+    "diffusion Monte Carlo",
+    "wave function optimization",
+    "pseudo potentials",
+    "probability density sampling",
+    "local maximization"
+  ]
+}

bib/MIT-aug-cc-pVTZ.abs

@@ -238,6 +238,12 @@ S GTO 9
    2.313000000000D-01   4.336405000000D-01
    1.026190000000D-01   2.131940000000D-01
    5.134400000000D-02   4.984800000000D-03
+S GTO 1
+   9.215520000000D-01   1.000000000000D+00
+S GTO 1
+   1.328000000000D-01   1.000000000000D+00
+S GTO 1
+   5.312000000000D-02   1.000000000000D+00
 P GTO 9
    9.934169000000D+00   2.090760000000D-02
    3.886955000000D+00   5.726980000000D-02
@@ -248,12 +254,6 @@ P GTO 9
    1.170630000000D-01   2.016934000000D-01
    5.854700000000D-02   4.535750000000D-02
    2.928100000000D-02   2.977500000000D-03
-S GTO 1
-   9.215520000000D-01   1.000000000000D+00
-S GTO 1
-   1.328000000000D-01   1.000000000000D+00
-S GTO 1
-   5.312000000000D-02   1.000000000000D+00
 P GTO 1
    3.767420000000D-01   1.000000000000D+00
 P GTO 1
@@ -271,3 +271,50 @@ F GTO 1
 F GTO 1
    3.093940000000D-01   1.000000000000D+00
 ****
+F
+S GTO 10
+   8.404865200000D+01  -2.800000000000D-06
+   4.109461700000D+01  -3.543000000000D-04
+   2.009273800000D+01   1.840880000000D-02
+   9.824112000000D+00  -1.277661000000D-01
+   4.803386000000D+00  -7.028720000000D-02
+   2.348560000000D+00   1.571604000000D-01
+   1.148301000000D+00   3.769012000000D-01
+   5.614490000000D-01   4.095165000000D-01
+   2.745140000000D-01   1.970893000000D-01
+   1.342200000000D-01   2.434820000000D-02
+S GTO 1
+   2.289795000000D+00   1.000000000000D+00
+S GTO 1
+   3.277120000000D-01   1.000000000000D+00
+S GTO 1
+   1.310850000000D-01   1.000000000000D+00
+P GTO 10
+   3.164261900000D+01   2.967300000000D-03
+   1.624323300000D+01   2.980490000000D-02
+   8.338204000000D+00   6.694890000000D-02
+   4.280284000000D+00   1.337790000000D-01
+   2.197215000000D+00   2.148312000000D-01
+   1.127906000000D+00   2.664862000000D-01
+   5.789920000000D-01   2.618954000000D-01
+   2.972160000000D-01   1.920217000000D-01
+   1.525710000000D-01   8.284650000000D-02
+   7.832000000000D-02   1.330460000000D-02
+P GTO 1
+   8.041810000000D-01   1.000000000000D+00
+P GTO 1
+   2.436600000000D-01   1.000000000000D+00
+P GTO 1
+   9.746400000000D-02   1.000000000000D+00
+D GTO 1
+   3.297425000000D+00   1.000000000000D+00
+D GTO 1
+   9.007630000000D-01   1.000000000000D+00
+D GTO 1
+   3.603050000000D-01   1.000000000000D+00
+F GTO 1
+   1.859274000000D+00   1.000000000000D+00
+F GTO 1
+   7.437100000000D-01   1.000000000000D+00
+****
+

bib/ecp/MIT.ecp

@@ -46,3 +46,13 @@
 1
 52.13345  2 7.76079
  ****
+
+####Fluorine
+9 2 1
+3
+7.0                 1 12.08758490486192
+84.61309433403344   3 12.83806306400466
+-53.02751706539332  2 12.31234562699041
+1
+78.90177172847011   2 14.78076492090162
+ ****

tools/Wfgen/Utils/__init__.py

@@ -1,7 +1,7 @@
 from .format import *
 from .data import *
 from .atom import Atom
-from .determinant import Determinant
+from .determinant import Determinant, build_det
 from .orbital import Orbital
 from .orbitalRotation import OrbitalRotation
 from .csf import Csf

tools/Wfgen/Utils/data.py

@@ -31,3 +31,14 @@
     [6,5,8,7,2,1,4,3],
     [7,8,5,6,3,4,1,2],
     [8,7,6,5,4,3,2,1]]
+
+# symmetries
+symmetries = {
+    'D2h':['Ag','B3u','B2u','B1g','B1u','B2g','B3g','Au'],
+    'C2v':['A1','B1','B2','A2'],
+    'C2h':['Ag','Au','Bu','Bg'],
+    'D2':['A','B3','B2','B1'],
+    'Cs':["A'","A''"],
+    'C2':['A','B'],
+    'Ci':['Ag','Au'],
+    'C1':['A']}

tools/Wfgen/Utils/determinant.py

@@ -54,3 +54,28 @@ def occupation_integer(self):
         for integer in self.orbital_list:
             occupation_string += str(abs(integer))
         return int(occupation_string)
+
+
+def build_det(number_inactive_orbitals,occupation,orbital_map,coefficient):
+    determinant = Determinant()
+    determinant.coefficient = coefficient
+    inactive_orbitals = []
+    j = 1
+    for _ in range(number_inactive_orbitals):
+        while j in orbital_map:
+            j += 1
+        inactive_orbitals.append(j)
+        j += 1
+    for inactive_orbital in inactive_orbitals:
+        determinant.orbital_list.append(inactive_orbital)
+        determinant.orbital_list.append(-inactive_orbital)
+    for i in range(len(occupation)):
+        if occupation[i] == '2':
+            determinant.orbital_list.append(orbital_map[i])
+            determinant.orbital_list.append(-orbital_map[i])
+        if occupation[i] == 'a':
+            determinant.orbital_list.append(orbital_map[i])
+        if occupation[i] == 'b':
+            determinant.orbital_list.append(-orbital_map[i])
+    determinant.sort()
+    return determinant

tools/Wfgen/Utils/waveFunction.py

@@ -213,7 +213,6 @@ def symm_combine(self):
             self.sort_dets()
             counter = 0
             orbital_groups = self.automatic_orbital_groups()
-            # print (orbital_groups)
 
             list_for_permutation = range(len(orbital_groups[0]))
             permutations = list(it.permutations(list_for_permutation))

tools/Wfgen/mol2wf.py

@@ -11,23 +11,6 @@
 from .Utils import *
 
 
-def build_det(number_core_orbitals,occupation,orbital_map,coefficient):
-    determinant = Determinant()
-    determinant.coefficient = coefficient
-    for i in range(number_core_orbitals):
-        determinant.orbital_list.append(i + 1)
-        determinant.orbital_list.append(-(i+1))
-    for i in range(len(occupation)):
-        if occupation[i] == '2':
-            determinant.orbital_list.append(orbital_map[i])
-            determinant.orbital_list.append(-orbital_map[i])
-        if occupation[i] == 'a':
-            determinant.orbital_list.append(orbital_map[i])
-        if occupation[i] == 'b':
-            determinant.orbital_list.append(-orbital_map[i])
-    determinant.sort()
-    return determinant
-
 def molpro_in(input_name,molden_name,basis,wf_type):
     out_filename = input_name + '.out'
     molden_filename = molden_name+'.molden'
@@ -232,7 +215,7 @@ def molpro_in(input_name,molden_name,basis,wf_type):
         if not line:
             sys.exit('Error: point group could not be read!')
     total_symmetry = line.split()[2]
-    symmetry_list = molpro_symmetries[total_symmetry]
+    symmetry_list = symmetries[total_symmetry]
 
     if wf_type != 'sd':
         #reading the symmetry of the occupied orbitals
@@ -383,24 +366,7 @@ def molpro_in(input_name,molden_name,basis,wf_type):
                         if words[0] == occupation_scheme:
                             spin_function = list(str(sf).split())
                     del spin_function[0]
-                    for j in range(len(spin_function)):
-                        occupation = list(csf_occupations[i])
-                        single_occupation = []
-                        letters = list(spin_function[j])
-                        for k in range(len(spin_function[j])):
-                            if letters[k] in ['a', 'b']:
-                                single_occupation.append(letters[k])
-                            elif letters[k] != '*':
-                                spin_coefficient += letters[k]
-                        coefficient = float(abs(Fraction(spin_coefficient)))**0.5 \
-                                      * int(Fraction(spin_coefficient)/abs(Fraction(spin_coefficient)))
-                        for k in range(len(occupation)):
-                            if occupation[k] in ['/', '\\']:
-                                occupation[k] = single_occupation[0]
-                                del single_occupation[0]
-                        determinant = build_det(number_core_orbitals, occupation, orbital_map, coefficient)
-                        csf.determinants.append(determinant)
-                        spin_coefficient = ''
+
 
                 else:  # if no singly occupied orbitals in csf
                     occupation = list(csf_occupations[i])
@@ -410,7 +376,24 @@ def molpro_in(input_name,molden_name,basis,wf_type):
 
                 csfs.append(csf)
                 occupation_scheme = ''
-
+                for j in range(len(spin_function)):
+                    occupation = list(csf_occupations[i])
+                    single_occupation = []
+                    letters = list(spin_function[j])
+                    for k in range(len(spin_function[j])):
+                        if letters[k] in ['a', 'b']:
+                            single_occupation.append(letters[k])
+                        elif letters[k] != '*':
+                            spin_coefficient += letters[k]
+                    coefficient = float(abs(Fraction(spin_coefficient)))**0.5 \
+                                  * int(Fraction(spin_coefficient)/abs(Fraction(spin_coefficient)))
+                    for k in range(len(occupation)):
+                        if occupation[k] in ['/', '\\']:
+                            occupation[k] = single_occupation[0]
+                            del single_occupation[0]
+                    determinant = build_det(number_core_orbitals, occupation, orbital_map, coefficient)
+                    csf.determinants.append(determinant)
+                    spin_coefficient = ''
     # construction for wf_type = 'sd'
     else:
         determinant = Determinant()
@@ -430,14 +413,3 @@ def molpro_in(input_name,molden_name,basis,wf_type):
     wf = WaveFunction(input_name, orbital_format, basis, charge, multiplicity, atoms, orbitals,
                       csfs, jastrow, total_symmetry, symmetry_list)
     return wf
-
-
-molpro_symmetries = {
-    'D2h':['Ag','B3u','B2u','B1g','B1u','B2g','B3g','Au'],
-    'C2v':['A1','B1','B2','A2'],
-    'C2h':['Ag','Au','Bu','Bg'],
-    'D2':['A','B3','B2','B1'],
-    'Cs':["A'","A''"],
-    'C2':['A','B'],
-    'Ci':['Ag','Au'],
-    'C1':['A']}