From b7cccee8783cd3a763aa76f4352fae32ca429ec1 Mon Sep 17 00:00:00 2001 From: Ask Hjorth Larsen Date: Wed, 12 Oct 2016 20:41:38 +0200 Subject: [PATCH] all molcas modules now either parsed or explicitly ignored. Typically parse the kind of method and the total energy. Relentlessly hacked SMs until the damn thing worked. --- parser/parser-molcas/main.py | 200 +++++++++++++++++++++++++------ parser/parser-molcas/runtests.py | 4 +- 2 files changed, 168 insertions(+), 36 deletions(-) diff --git a/parser/parser-molcas/main.py b/parser/parser-molcas/main.py index 3bd017c..ff980f0 100755 --- a/parser/parser-molcas/main.py +++ b/parser/parser-molcas/main.py @@ -113,8 +113,14 @@ class MolcasContext(object): # XXX distinguish somehow between these two? esm = 'DFT' xc = ['HF_X'] - elif method in ['RASSCF', 'RAS-CI', 'CASPT2']: + elif method in ['RASSCF', 'RAS-CI', 'CASPT2', 'CCSDT']: esm = method + elif method in ['CASVB', 'MRCI']: + esm = 'MRCISD' + elif method == 'MCPF': + esm = method ## Not defined by nomad + elif method == 'MBPT2': + esm = 'MP2' elif method in functionals: esm = 'DFT' xc = functionals[method] @@ -216,12 +222,12 @@ class MolcasContext(object): context = MolcasContext() -def get_inputfile_echo_sm(): - m = SM(r'\+\+\s*----+\s*Input file\s*---+', - endReStr='--\s*-------+', - sections=['section_method'], - name='inputfile') - return m +#def get_inputfile_echo_sm(): +# m = SM(r'\+\+\s*----+\s*Input file\s*---+', +# endReStr='--\s*-------+', +# sections=['section_method'], +# name='inputfile') +# return m def get_system_sm(): @@ -247,7 +253,7 @@ def get_finalresults_sm(): # Other modes than SCF/KS-DFT? sections=['section_single_configuration_calculation'], name='results', subMatchers=[ - SM(r'\s*Total SCF energy\s*(?P\S+)', name='etot') # XXX eV? + SM(r'\s*Total SCF energy\s*(?P\S+)', name='etot') ]) return m @@ -267,12 +273,36 @@ molcas_modules = ('alaska|caspt2|casvb|ccsdt|cpf|expbas|ffpt|gateway|' 'mckinley|mclr|motra|mrci|numerical_gradient|rasscf|' 'rassi|scf|seward|slapaf|vibrot').split('|') +ignore_modules = {'alaska', # OK + 'numerical_gradient', # OK + 'rassi', # OK + 'motra', + 'guga', + 'ffpt', + 'genano', + 'grid_it', + 'loprop', + 'guessorb', + 'expbas', + 'vibrot', + 'mckinley' + #'last_energy', +} + def get_anymodule_sms(): sms = [] for modulename in molcas_modules: - sms.append(SM(r'--- Start Module:\s*%s' % modulename, name=modulename)) - #sms.append(SM(r'\s*MOLCAS executing module %s' % modulename.upper(), - # name=modulename)) + adhoc = None + if modulename not in ignore_modules: + class AdHoc: + def __init__(self, name): + self.name = name + def __call__(self, parser): + raise ValueError('module: %s' % self.name) + adhoc = AdHoc(modulename) + sms.append(SM(r'--- Start Module:\s*%s' % modulename, + adHoc=adhoc, + name=modulename)) return sms #def module_sm(name, *args, **kwargs): @@ -295,6 +325,57 @@ def mw(modname, *args, **kwargs): ]) return m +def mod_pattern(lower, upper=None): + if upper is None: + upper = lower.upper() + return (r'---\s*Start Module:\s*{0}|' + r'\s*MOLCAS executing module\s*{1}'.format(lower, upper)) + +# Define these separately or not? +def startmod_pattern(name): + return r'---\s*Start Module:\s*{}'.format(name) +def execmod_pattern(name): + return r'\s*MOLCAS executing module\s*{}'.format(name) + +def gateway_seward(): + m = SM(mod_pattern(r'(:?gateway|seward)'), + #weak=True, + name='gate/seward', + #r'\s*MOLCAS executing module (GATEWAY|SEWARD)', name='seward', + subMatchers=[ + get_system_sm() + ]) + return m + +def scf_rasscf(): + m = SM(mod_pattern(r'(:?ras)?scf'), + name='(ras)scf', #r'(?:ras)?scf', r'\s*MOLCAS executing module (?:SCF|RASSCF)', name='scf', + #sections=['section_method', 'section_single_configuration_calculation'], + subMatchers=[ # XXX opens method section even if there is no outpout + SM(r'\s*(?P.*?)\s*iterations: Energy and convergence statistics', + sections=['section_method'], + name='scfiter'), + SM(r'\s*CI only, no orbital optimization', + sections=['section_method'], + fixedStartValues={'x_molcas_method_name': 'RAS-CI'}), + SM(r'\s*Total SCF energy\s*(?P\S+)', name='E-tot', + sections=['section_single_configuration_calculation']), + SM(r'\s*RASSCF root number\s*\d+\s*Total energy\s*=\s*(?P\S+)', name='E-ras', + sections=['section_single_configuration_calculation']), + ]) + return m + +def caspt2(): + m = SM(mod_pattern(r'caspt2'), + #caspt2', r'\s*MOLCAS executing module CASPT2', + name='caspt2', # XXX opens section even if there is no output + sections=['section_method', 'section_single_configuration_calculation'], + fixedStartValues={'x_molcas_method_name': 'CASPT2'}, + subMatchers=[ + SM(r'\s*Total energy:\s*(?P\S+)', name='E-caspt2') + ]) + return m + def molcas_main_loop_sm(): m = SM(r'--- Start Module:\s*(?:%s)' % '|'.join(molcas_modules), endReStr='--- Stop Module:', @@ -302,29 +383,12 @@ def molcas_main_loop_sm(): forwardMatch=True, name='module', subMatchers=[ - mw(r'(gateway|seward)', - r'\s*MOLCAS executing module (GATEWAY|SEWARD)', name='seward', - subMatchers=[ - get_system_sm() - ]), - mw(r'(?:ras)?scf', r'\s*MOLCAS executing module (?:SCF|RASSCF)', name='scf', - sections=['section_method', 'section_single_configuration_calculation'], - subMatchers=[ - SM(r'\s*(?P.*?)\s*iterations: Energy and convergence statistics', - name='scfiter'), - SM(r'\s*CI only, no orbital optimization', - fixedStartValues={'x_molcas_method_name': 'RAS-CI'}), - SM(r'\s*Total SCF energy\s*(?P\S+)', name='E-tot'), - SM(r'\s*RASSCF root number\s*\d+\s*Total energy\s*=\s*(?P\S+)', name='E-ras'), - ]), - mw(r'caspt2', r'\s*MOLCAS executing module CASPT2', - name='caspt2', - sections=['section_method', 'section_single_configuration_calculation'], - fixedStartValues={'x_molcas_method_name': 'CASPT2'}, - subMatchers=[ - SM(r'\s*Total energy:\s*(?P\S+)', name='E-caspt2') - ]), - mw(r'slapaf', r'\s*MOLCAS executing module (SLAPAF)|\s*Specification of the internal coordinates according to the user-defined', + gateway_seward(), + scf_rasscf(), + caspt2(), + SM(r'%s|%s' % (mod_pattern(r'slapaf'), + # Sometimes the damn thing starts without a proper header!! ARGH! + r's*Specification of the internal coordinates according to the user-defined'), name='slapaf', subMatchers=[ SM(r'\*\s*Energy Statistics for Geometry Optimization', @@ -345,7 +409,73 @@ def molcas_main_loop_sm(): r'\s*ATOM\s*X\s*Y\s*Z', r'\s*(\S+)\s*(\S+)\s*(\S+)\s*(\S+)') ]) - ]) + ]), + # last_energy just means it calls some other modules with annoyingly irregular output format + SM(mod_pattern(r'last_energy'), + name='last', + subMatchers=[ + gateway_seward(), + scf_rasscf(), + caspt2(), + ]), + SM(mod_pattern('casvb'), + name='casvb', + sections=['section_method'], + fixedStartValues={'x_molcas_method_name': 'CASVB'}, + subMatchers=[ + SM('\s*CASSCF energy\s*:\s*(?P\S+)', + sections=['section_single_configuration_calculation'], + name='e-tot') + ]), + SM(mod_pattern('mrci'), + name='mrci', + sections=['section_method'], + fixedStartValues={'x_molcas_method_name': 'MRCI'}, + subMatchers=[ + SM(r'\s*CI ENERGY:\s*(?P\S+)', + sections=['section_single_configuration_calculation']) + ]), + SM(mod_pattern('cpf', 'CPFMCPF'), + name='cpf', + sections=['section_method'], + fixedStartValues={'x_molcas_method_name': 'MCPF'}, + subMatchers=[ + SM(r'\s*FINAL MCPF ENERGY\s*(?P\S+)', + sections=['section_single_configuration_calculation']) + ]), + SM(mod_pattern('ccsdt', r'CCSD\(T\)'), + name='ccsdt', + sections=['section_method'], + fixedStartValues={'x_molcas_method_name': 'CCSDT'}, + subMatchers=[ + SM(r'\s*Total energy \(diff\)\s*:\s*(?P\S+)', + sections=['section_single_configuration_calculation']) + ]), + SM(mod_pattern('mbpt2'), + name='mbpt2', + fixedStartValues={'x_molcas_method_name': 'MBPT2'}, + sections=['section_method', 'section_single_configuration_calculation'], + subMatchers=[ + SM(r'\s*Total energy\s*=\s*(?P\S+)\s*a\.u\.') + ]), + SM(mod_pattern('mclr'), + name='mclr', + subMatchers=[ + SM(r'\s*\*\s*Harmonic frequencies in cm-1\s*\*', + endReStr=r'\s*\*\s*THERMOCHEMISTRY', + sections=['section_single_configuration_calculation'], + subMatchers=[ + SM(r'\s*Symmetry\s*(?P\S+)', + name='symm', + repeats=True, + sections=['x_molcas_section_frequency'], + subMatchers=[ + SM(r'\s*Freq\.\s*i(?P\S+)', name='ifreq'), + SM(r'\s*Freq\.\s*(?P\S+)', name='freq'), + SM(r'\s*Intensity:\s*(?P\S+)', name='intensity') + ]) + ]), + ]), ] + get_anymodule_sms()) return m diff --git a/parser/parser-molcas/runtests.py b/parser/parser-molcas/runtests.py index 23b4d4b..7e18fc2 100755 --- a/parser/parser-molcas/runtests.py +++ b/parser/parser-molcas/runtests.py @@ -38,12 +38,14 @@ for i, testfile in enumerate(testfiles): if i % world.size != world.rank: continue dirname, basename = os.path.split(testfile) - print(basename) + #print(testfile) + #print(basename) py = 'python' if platform.node() == 'labdev-nomad': py = '/labEnv3/bin/python' args = [py, 'main.py', '--annotate'] args.append(testfile) + print(' '.join(args)) proc = Popen(args, stdout=PIPE) txt = proc.stdout.read() with open('%s.json' % testfile, 'w') as fd: -- GitLab