add more templates

Konjkov · Sep 8, 2019 · 0d121e3 · 0d121e3
1 parent d66ac54
commit 0d121e3
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Showing 8 changed files with 99 additions and 21 deletions.
diff --git a/ADF/Snakefile b/ADF/Snakefile
@@ -37,8 +37,8 @@ rule ALL_VMC_DMC:
 rule ALL_VMC_DMC_BF:
     input:
         expand('{method}/{basis}/{molecule}/VMC_DMC_BF/emin_BF/{jastrow}__9_9_33/tmax_1_1024_2/out', method=METHODS, basis=BASES, molecule=MOLECULES, jastrow=JASTROWS),
-#        expand('{method}/{basis}/{molecule}/VMC_DMC_BF/emin_BF/{jastrow}__9_9_33/tmax_2_2048_2/out', method=METHODS, basis=BASES, molecule=MOLECULES, jastrow=JASTROWS),
-#        expand('{method}/{basis}/{molecule}/VMC_DMC_BF/emin_BF/{jastrow}__9_9_33/tmax_4_4096_2/out', method=METHODS, basis=BASES, molecule=MOLECULES, jastrow=JASTROWS),
+        expand('{method}/{basis}/{molecule}/VMC_DMC_BF/emin_BF/{jastrow}__9_9_33/tmax_2_2048_2/out', method=METHODS, basis=BASES, molecule=MOLECULES, jastrow=JASTROWS),
+        expand('{method}/{basis}/{molecule}/VMC_DMC_BF/emin_BF/{jastrow}__9_9_33/tmax_4_4096_2/out', method=METHODS, basis=BASES, molecule=MOLECULES, jastrow=JASTROWS),
 
 rule ALL_VMC_OPT_ENERGY:
     input:
@@ -68,14 +68,19 @@ rule MDET:
     shell:      'cd "$(dirname "{output}")" && multideterminant.py 0 output.dat'
 
 rule WFN:
-    input:      '{method}/{basis}/{molecule}/TAPE21.asc'
+    input:      '{method}/{basis}/{molecule}/output.dat'
     output:     '{method}/{basis}/{molecule}/stowfn.data'
     shell:      'cd "$(dirname "{output}")" && adf2stowf.py'
 
-rule TAPE21:
-    input:      '{method}/{basis}/{molecule}/output.dat'
-    output:     '{method}/{basis}/{molecule}/TAPE21.asc'
-    shell:      'dmpkf "$(dirname "{output}")/TAPE21" > "{output}"'
+#rule WFN:
+#    input:      '{method}/{basis}/{molecule}/TAPE21.asc'
+#    output:     '{method}/{basis}/{molecule}/stowfn.data'
+#    shell:      'cd "$(dirname "{output}")" && adf2stowf.py'
+
+#rule TAPE21:
+#    input:      '{method}/{basis}/{molecule}/output.dat'
+#    output:     '{method}/{basis}/{molecule}/TAPE21.asc'
+#    shell:      'dmpkf "$(dirname "{output}")/TAPE21" > "{output}"'
 
 rule ADF_RUN:
     input:      '{path}/input.dat'
@@ -103,7 +108,7 @@ rule ADF_INPUT:
             f.write(open('adf.tmpl').read().format(
                 basis=basis,
                 core=core,
-                method=wildcards.method,
+                method=wildcards.method.replace('_', ' '),
                 molecule=wildcards.molecule,
                 charge=charge,
                 a_minus_b=multiplicity-1,

diff --git a/ADF/config.yaml b/ADF/config.yaml
@@ -1,11 +1,7 @@
 STD_ERR: 0.0001
 VMC_NCONFIG: 100000
-#MOLECULES: ['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'P', 'Cl', 'Ar']
-#MOLECULES: ['K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr']
+MOLECULES: ['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'P', 'Cl', 'Ar']
+MOLECULES: ['K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr']
 METHODS: ['HartreeFock']
-#BASES: ['DZ', 'TZP', 'TZ2P', 'QZ4P']
-BASES: ['QZ4P']
-#MOLECULES: ['Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe']
-MOLECULES: ['O3']
-#BASES: ['ZORA_DZ', 'ZORA_TZP', 'ZORA_TZ2P', 'ZORA_QZ4P']
+BASES: ['DZ', 'TZP', 'TZ2P', 'QZ4P']
 JASTROWS: ['8_8_44']
diff --git a/ADF/config_zora.yaml b/ADF/config_zora.yaml
@@ -0,0 +1,6 @@
+STD_ERR: 0.0001
+VMC_NCONFIG: 100000
+MOLECULES: ['Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe']
+METHODS: ['HartreeFock']
+BASES: ['ZORA_DZ', 'ZORA_TZP', 'ZORA_TZ2P', 'ZORA_QZ4P']
+JASTROWS: ['8_8_44']
diff --git a/ORCA/Snakefile b/ORCA/Snakefile
@@ -175,9 +175,8 @@ rule MOLDEN:
         elif 'NEVPT2' in wildcards.method:
             shell("""
                   cd "$(dirname "{output}")"
-                  ln -s nevpt2.PT2.*.nat nevpt2.nat.gbw &&
-                  $(which orca_2mkl) nevpt2.nat -molden &&
-                  ln -s nevpt2.nat.molden.input mol.molden.input""")
+                  $(which orca_2mkl) nevpt2 -molden &&
+                  ln -s nevpt2.molden.input mol.molden.input""")
         else:
             shell("""
                   cd "$(dirname "{output}")"
@@ -216,6 +215,8 @@ rule ORCA_RUN:
             method = wildcards.method.split('-NEVPT2')[0]
             if method in ('MP2', 'OO-RI-MP2'):
                 moinp = 'mol.mp2nat'
+            else:
+                moinp = 'mol.qro'
             irrep = get_irrep(os.path.join(wildcards.method, wildcards.basis, wildcards.molecule))
             with open(os.path.join(wildcards.method, wildcards.basis, wildcards.molecule, 'nevpt2.inp'), 'w') as f:
                 offset = wildcards.method.find('(') + 1

diff --git a/QCHEM/Snakefile b/QCHEM/Snakefile
@@ -131,10 +131,11 @@ rule QCHEM_RUN:
                 template = 'qchem_multideterminant.tmpl'
             else:
                 method = wildcards.method
-                if stability_analysis == 'true':
-                    template = 'qchem.tmpl'
-                else:
+                if stability_analysis:
                     template = 'qchem_unstable.tmpl'
+                else:
+                    template = 'qchem.tmpl'
+#                    template = 'qchem_geminals.tmpl'
             with open(input[0], 'r') as f:
                 f.readline()                   # skip first line
                 molecule_data = f.read()[:-1]  # skip last NL
@@ -183,6 +184,7 @@ rule QCHEM_RUN:
                         method=method,
                         molecule_data=molecule_data,
                         algorithm=algorithm,
+                        unrestricted='true',
                         stability_analysis=stability_analysis
                     ))
             shell('qchem -nt 4 "{qchem_input}" "{output}"')

diff --git a/QCHEM/config.yaml b/QCHEM/config.yaml
@@ -0,0 +1,6 @@
+STD_ERR: 0.0001
+VMC_NCONFIG: 100000
+MOLECULES: ['C2']
+METHODS: ['HF']
+BASES: ['cc-pVDZ']
+JASTROWS: ['8_8_44']
diff --git a/QCHEM/qchem_geminals.tmpl b/QCHEM/qchem_geminals.tmpl
@@ -0,0 +1,39 @@
+$comment
+qchem input for CASINO geminals
+$end
+
+$rem
+SYMMETRY              true
+BASIS                 {basis}
+METHOD                {method}
+MAX_SCF_CYCLES        100
+SCF_CONVERGENCE       8
+SCF_ALGORITHM         {algorithm}
+UNRESTRICTED          {unrestricted}
+MEM_STATIC            2000
+STABILITY_ANALYSIS    {stability_analysis}
+$end
+
+$molecule
+{molecule_data}
+$end
+
+@@@
+
+$rem
+SYMMETRY              true
+SSG                   1
+SSG_ARAI_OPT          0
+BASIS                 {basis}
+METHOD                {method}
+SCF_GUESS             read
+SCF_CONVERGENCE       8
+UNRESTRICTED          {unrestricted}
+MAX_SCF_CYCLES        200
+MOLDEN_FORMAT         true
+PRINT_ORBITALS        2000
+$end
+
+$molecule
+{molecule_data}
+$end
diff --git a/QCHEM/qchem_geminals_simple.tmpl b/QCHEM/qchem_geminals_simple.tmpl
@@ -0,0 +1,23 @@
+$comment
+qchem input for CASINO geminals
+$end
+
+$rem
+SYMMETRY              true
+BASIS                 {basis}
+METHOD                {method}
+SSG                   true
+SCF_GUESS             sadmo
+MAX_SCF_CYCLES        100
+SCF_CONVERGENCE       8
+SCF_ALGORITHM         {algorithm}
+MEM_STATIC            2000
+STABILITY_ANALYSIS    {stability_analysis}
+SET_ITER              100
+MOLDEN_FORMAT         true
+PRINT_ORBITALS        2000
+$end
+
+$molecule
+{molecule_data}
+$end