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nwc: add hessian file; minor testing updates #177

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merged 27 commits into from
Dec 5, 2019
Merged

nwc: add hessian file; minor testing updates #177

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0e002c1
nwc: add tce dipole harvest
vivacebelles Jul 3, 2019
7af1322
nwc: add tce dipole harvest
vivacebelles Jul 16, 2019
970d15c
Merge branch 'master' of https://github.com/MolSSI/QCEngine into nwc
vivacebelles Jul 16, 2019
0cc9ccc
Merge branch 'nwc' of https://github.com/vivacebelles/QCEngine into nwc
vivacebelles Jul 16, 2019
a1707c2
nwc: dipole regex edit
vivacebelles Jul 19, 2019
064624e
nwc: add tce dipole harvest
vivacebelles Jul 3, 2019
2121502
nwc: add tce dipole harvest
vivacebelles Jul 16, 2019
b89f413
nwc: dipole regex edit
vivacebelles Jul 19, 2019
c266d5d
nwc: add keep file for running hess, adjust harvester'
vivacebelles Oct 18, 2019
45c4f8a
merge conflicts
vivacebelles Oct 28, 2019
848cb14
Merge branch 'master' into nwc
vivacebelles Nov 18, 2019
8a0dbdb
nwc: add tddft to germinate; rm specific qcdb opts for basis set
vivacebelles Nov 18, 2019
0333bce
merge conflicts
vivacebelles Nov 18, 2019
835255b
nwc: regex edits to tddft, eom (wip)
vivacebelles Nov 27, 2019
3fd4228
nwc:tddft regex edit (wip)
vivacebelles Dec 2, 2019
528d07d
nwc: eom + tddft regex + vars (wip)
vivacebelles Dec 3, 2019
00af3f2
nwc: add tce dipole harvest
vivacebelles Jul 3, 2019
5b334f1
nwc: add tce dipole harvest
vivacebelles Jul 16, 2019
dda118e
nwc: dipole regex edit
vivacebelles Jul 19, 2019
b9860bd
nwc: add tce dipole harvest
vivacebelles Jul 3, 2019
c8f21c1
nwc: add tce dipole harvest
vivacebelles Jul 16, 2019
6985d0c
nwc: add keep file for running hess, adjust harvester'
vivacebelles Oct 18, 2019
adb8fca
nwc: regex edits to tddft, eom (wip)
vivacebelles Nov 27, 2019
bded756
nwc:tddft regex edit (wip)
vivacebelles Dec 2, 2019
b62c81d
nwc: eom + tddft regex + vars (wip)
vivacebelles Dec 3, 2019
9ec37fc
black: nwc files
vivacebelles Dec 3, 2019
5c3049b
black: nwc & resolve merge conflicts
vivacebelles Dec 3, 2019
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nwc: add keep file for running hess, adjust harvester'
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@vivacebelles
vivacebelles committed Oct 22, 2019
commit c266d5d27dda519c44e3779bc0196d24dd68fc11
14 changes: 7 additions & 7 deletions qcengine/programs/nwchem/harvester.py
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Original file line number Diff line number Diff line change
Expand Up @@ -199,7 +199,7 @@ def harvest_outfile_pass(outtext):
psivar[f'{mbpt_plain} TOTAL ENERGY'] = mobj.group(2)
#TCE dipole- MBPT(n)
mobj2 = re.search(
r'^\s+' + cc_name + r'dipole moments / hartree & Debye' + r'\s*' +
r'^\s+' + r'dipole moments / hartree & Debye' + r'\s*' +
r'^\s+' + r'X' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'Y' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'Z' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
Expand Down Expand Up @@ -264,19 +264,19 @@ def harvest_outfile_pass(outtext):
psivar[f'{cc_name} TOTAL ENERGY'] = mobj.group(2)
#TCE dipole
mobj2 = re.search(
r'^\s+' + cc_name + r'dipole moments / hartree & Debye' + r'\s*' +
r'^\s+' + r'dipole moments / hartree & Debye' + r'\s*' +
r'^\s+' + r'X' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'Y' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'Z' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'Total' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE)
if mobj2:
print(f'matched tce {cc_name} dipole moment')
print(f'matched tce dipole moment')

#only pulling Debye
psivar[f'{cc_name} DIPOLE X'] = mobj2.group(2)
psivar[f'{cc_name} DIPOLE Y'] = mobj2.group(4)
psivar[f'{cc_name} DIPOLE Z'] = mobj2.group(6)
psivar[f'CURRENT DIPOLE X'] = mobj2.group(2)
psivar[f'CURRENT DIPOLE Y'] = mobj2.group(4)
psivar[f'CURRENT DIPOLE Z'] = mobj2.group(6)

# Process CCSD/CCSD(T) using nwchem CCSD/CCSD(T) [dertype] command
mobj = re.search(
Expand Down Expand Up @@ -542,7 +542,7 @@ def harvest_outfile_pass(outtext):
atoms.append(lline[1]) # Tag
psivar_grad.append([float(lline[-3]), float(lline[-2]), float(lline[-1])])

# Process dipole
# Process dipole (Properties)
mobj = re.search(
r'^\s+' + r'Dipole moment' + r'\s+' + NUMBER + r'\s+' + r'A\.U\.' + r'\s*' +
r'^\s+' + r'DMX' + r'\s+' + NUMBER + r'.*' +
Expand Down
7 changes: 5 additions & 2 deletions qcengine/programs/nwchem/runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,10 @@ def build_input(self, input_model: 'ResultInput', config: 'JobConfig',
# Handle basis set
# * for nwchem, still needs sph and ghost
for el in set(input_model.molecule.symbols):
opts[f'basis__{el}'] = f'library {input_model.model.basis}'
if ropts.scrolls['QCDB']['BASIS'] == "nwchem-{el}":
opts[f'basis_nwchem-{el}'] = f'library {input_model.model.basis}'
else:
opts[f'basis__{el}'] = f'library {input_model.model.basis}'

print('JOB_OPTS')
pp.pprint(opts)
Expand All @@ -139,7 +142,7 @@ def execute(self,
success, dexe = execute(
inputs["command"],
inputs["infiles"],
["job.movecs", "job.hess", "job.db", "job.zmat"],
["job.movecs", "job.hess", "job.db", "job.zmat", "job.fd_dipole"],
scratch_messy=False,
scratch_directory=inputs["scratch_directory"],
)
Expand Down