def main():
common.parser().add_option("--indb", dest="indb", help="Input database")
if not common.init(__file__):
exit(2)
progname = common.progname()
indb = common.options().indb
if not indb:
indb = common.testdir() + "/pgn/Kramnik.pgn"
temppgn1 = common.tmpdir() + "/copydb1.pgn"
temppgn2 = common.tmpdir() + "/copydb2.pgn"
tempcfdb1 = common.tmpdir() + "/copydb1.cfdb"
if run(1, indb, tempcfdb1) and run(2, tempcfdb1, temppgn1) and run(3, indb, temppgn2):
# temppgn1 and temppgn2 should be identical
if os.path.exists(temppgn1) and os.path.exists(temppgn2):
lines1 = open(temppgn1, "U").readlines()
lines2 = open(temppgn2, "U").readlines()
diff = difflib.unified_diff(lines1, lines2)
different = False
first = True
for line in diff:
if first:
print "{0}: PGN files {1} and {2} are different:".format(progname, temppgn1, temppgn2)
different = True
first = False
print line
if not different:
print "{0}: Test successful".format(progname)
else:
print "{0}: Failed; no output files to compare".format(progname)
def main():
common.parser().add_option("--indb", dest = "indb", help = "Input database")
common.parser().add_option("--outdb", dest = "outdb", help = "Output database")
common.parser().add_option("--firstgame", dest="firstgame", help = "First game in input database to analyze")
common.parser().add_option("--lastgame", dest="lastgame",help = "First game in input database to analyze")
common.parser().add_option("--ecofile", dest = "ecofile", help = "The (.cfdb) database containing the ECO classification")
if not common.init(__file__):
exit(2)
progname = common.progname()
debuglog = True
logcomms = False
logfile1 = common.tmpdir() + "/ccore1.log"
logfile2 = common.tmpdir() + "/ccore2.log"
configfile = common.configfile()
indb = common.options().indb
if not indb:
indb = common.testdir() + "/pgn/Boris_Spassky.pgn"
outdb = common.options().outdb
if not outdb:
outdb = common.tmpdir() + "/classified.cfdb"
if os.path.exists(outdb):
os.remove(outdb)
ecofile = common.options().ecofile
if not ecofile:
ecofile = common.testdir() + "/cfdb/eco.cfdb"
firstgame = common.options().firstgame
lastgame = common.options().lastgame
if os.path.exists(logfile1):
os.remove(logfile1)
if os.path.exists(logfile2):
os.remove(logfile2)
# Take a copy of the database
cmdline = common.ccore()
if debuglog:
cmdline += " --debuglog true"
if logcomms:
cmdline += " --logcomms true"
if firstgame:
cmdline += " -n {0}".format(firstgame)
if lastgame:
cmdline += " -N {0}".format(lastgame)
cmdline += " -l {0} -i {1} -o {2} copydb".format(logfile1, indb, outdb);
if common.runccore(cmdline):
common.checkLogfile(logfile1)
# And then classify the copy
cmdline = common.ccore()
if debuglog:
cmdline += " --debuglog true"
if logcomms:
cmdline += " --logcomms true"
cmdline += " -l {0} -i {1} -E {2} classify".format(logfile2, outdb, ecofile)
if common.runccore(cmdline):
common.checkLogfile(logfile2)
def main():
common.parser().add_option("--epdfile", dest = "epdfile", help = "Input EPD file")
common.parser().add_option("--timecontrol", dest="timecontrol", default = "10s", help = "Time control")
common.parser().add_option("--engine", dest="engine", help = "The engine to use to process the EPD file")
if not common.init(__file__):
exit(2)
progname = common.progname()
debuglog = True
logcomms = False
logfile = common.tmpdir() + "/ccore.log"
configfile = common.configfile()
epdfile = common.options().epdfile
if not epdfile:
usage()
timecontrol = common.options().timecontrol
engine = common.options().engine
if not engine:
engine = common.engine1()
if os.path.exists(logfile):
os.remove(logfile)
# Take a copy of the database
cmdline = common.ccore()
if debuglog:
cmdline += " --debuglog true"
if logcomms:
cmdline += " --logcomms true"
cmdline += " -c {0} -l {1} -e {2} -t {3} processepd {4}".format(configfile, logfile, epdfile, timecontrol, engine);
if common.runccore(cmdline):
common.checkLogfile(logfile)
def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
name = 'uio66-zr-brick/system.chk'
fn = context.get_fn(os.path.join('systems', name))
data = load_chk(fn)
system = System(data['numbers'],data['pos'],charges=data['charges'],
ffatypes=data['ffatypes'],bonds=data['bonds'],radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai', coords=system.pos.copy(),
grad=data['gradient'], hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,fn_yaff=fn_yaff,fn_sys=fn_sys,log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s"%("Basename","Cross FC","Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0,1]:
fc_diag = program.valence.get_params(term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" % (term.basename,fc,fc_diag,program.valence.terms[term.diag_term_indexes[i]].basename))
if fc_diag==0.0: assert fc==0.0
def main():
common.parser().add_option("--indb", dest = "indb", help = "Input database")
common.parser().add_option("--outdb", dest = "outdb", help = "Output database")
if not common.init(__file__):
exit(2)
progname = common.progname()
debuglog = True
logfile1 = common.tmpdir() + "/ccore1.log"
logfile2 = common.tmpdir() + "/ccore2.log"
indb = common.options().indb
if not indb:
indb = common.rootdir() + "/doc/OpeningClassification/eco.pgn"
outdb = common.options().outdb
if not outdb:
outdb = common.testdir() + "/cfdb/eco.cfdb"
if os.path.exists(logfile1):
os.remove(logfile1)
if os.path.exists(logfile2):
os.remove(logfile2)
if os.path.exists(outdb):
os.remove(outdb)
# Copy the database
cmdline = common.ccore()
if debuglog:
cmdline += " --debuglog true"
cmdline += " -l {0} -i {1} -o {2} copydb".format(logfile1, indb, outdb)
if common.runccore(cmdline):
common.checkLogfile(logfile1)
# Create the opening tree in the output database
cmdline = common.ccore()
if debuglog:
cmdline += " --debuglog true"
cmdline += " -l {0} -i {1} -d 100 buildoptree".format(logfile2, outdb)
if common.runccore(cmdline):
common.checkLogfile(logfile2)
def main():
common.parser().add_option("--engine1", dest = "engine1", help = "Engine #1")
common.parser().add_option("--engine2", dest = "engine2", help = "Engine #2")
common.parser().add_option("--numgames", dest = "numgames", type = "int", default = 5, help = "Number of games")
common.parser().add_option("--timecontrol", dest = "timecontrol", default = "30", help = "Time control")
common.parser().add_option("--ecofile", dest = "ecofile", help = "The (.cfdb) database containing the ECO classification")
common.parser().add_option("--logcomms", dest = "logcomms", type = "int", default = 0, help = "Log UCI comms")
if not common.init(__file__):
exit(2)
progname = common.progname()
debuglog = True
logcomms = common.options().logcomms != 0
logfile = common.tmpdir() + "/ccore.log"
pgnfile = common.tmpdir() + "/games.pgn"
configfile = common.configfile()
ecofile = common.options().ecofile
if not ecofile:
ecofile = common.testdir() + "/cfdb/eco.cfdb"
engine1 = common.options().engine1
if not engine1:
engine1 = common.engine1()
engine2 = common.options().engine2
if not engine2:
engine2 = common.engine2()
numgames = common.options().numgames
timecontrol = common.options().timecontrol
if os.path.exists(logfile):
os.remove(logfile)
cmdline = common.ccore()
if debuglog:
cmdline += " --debuglog true"
if logcomms:
cmdline += " --logcomms true"
cmdline += " -c {0} -l {1} -o {2} -E {3} -n {4} -t {5} tournament {6} {7}".format(configfile, logfile, pgnfile, ecofile, numgames, timecontrol, engine1, engine2)
if common.runccore(cmdline):
common.checkLogfile(logfile)
def test_methane_consistent_crossterms():
with log.section('NOSETEST', 2):
system, ai = read_system('methane/gaussian.fchk')
set_ffatypes(system, 'high')
for consistent in [False, True]:
with tmpdir('test_methane_%s'%('consistent' if consistent else 'inconsistent')) as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=consistent,
fn_yaff=fn_yaff,fn_sys=fn_sys,do_cross_DSS=True,do_cross_DSD=True,
do_cross_DAA=True,do_cross_DAD=True))
program.run()
compare_crossterm_rest_values(program,equal=consistent)
def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
name = 'uio66-zr-brick/system.chk'
fn = context.get_fn(os.path.join('systems', name))
data = load_chk(fn)
system = System(data['numbers'],
data['pos'],
charges=data['charges'],
ffatypes=data['ffatypes'],
bonds=data['bonds'],
radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai',
coords=system.pos.copy(),
grad=data['gradient'],
hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(
system, ai,
Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,
fn_yaff=fn_yaff,
fn_sys=fn_sys,
log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s" % ("Basename", "Cross FC", "Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0, 1]:
fc_diag = program.valence.get_params(
term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" %
(term.basename, fc, fc_diag, program.valence.terms[
term.diag_term_indexes[i]].basename))
if fc_diag == 0.0: assert fc == 0.0
def compile(stack, args):
extraOpts = []
skip_flags = os.environ.get('SKIP_FLAGS', '')
if skip_flags:
extraOpts += skip_flags.split(',')
output = stack.enter_context(common.tmpdir(prefix='tmp.js_exec.'))
cmd = [
os.path.join(common.build_dir, 'bin/skip_to_js'), '--output',
output + '/sk.js', '--no-source-map'
] + extraOpts + args.srcs
logger.debug('Running: ' + ' '.join(map(pipes.quote, cmd)))
with common.PerfTimer('skip_to_js.runtime'):
common.callHelper(cmd)
return [
common.root_dir + '/tools/run_js', '--no-unhandled-exception-stack',
output
]
def test_methane_consistent_crossterms():
with log.section('NOSETEST', 2):
system, ai = read_system('methane/gaussian.fchk')
set_ffatypes(system, 'high')
for consistent in [False, True]:
with tmpdir(
'test_methane_%s' %
('consistent' if consistent else 'inconsistent')) as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
program = DeriveFF(
system, ai,
Settings(consistent_cross_rvs=consistent,
fn_yaff=fn_yaff,
fn_sys=fn_sys,
do_cross_DSS=True,
do_cross_DSD=True,
do_cross_DAA=True,
do_cross_DAD=True))
program.run()
compare_crossterm_rest_values(program, equal=consistent)
def test_output_charmm22():
with log.section('NOSETST', 2):
system, ai = read_system('ethanol/gaussian.fchk')
set_ffatypes(system, 'low')
with tmpdir('test_output_charmm22') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_charmm22_prm = os.path.join(dn, 'test.prm')
fn_charmm22_psf = os.path.join(dn, 'test.psf')
fn_sys = os.path.join(dn, 'system.chk')
settings = Settings(
do_cross_ASS=False, do_cross_ASA=False,
fn_yaff=fn_yaff, fn_sys=fn_sys,
fn_charmm22_prm=fn_charmm22_prm,
fn_charmm22_psf=fn_charmm22_psf,
)
program = DeriveFF(system, ai, settings)
program.run()
assert os.path.isfile(fn_yaff)
assert os.path.isfile(fn_charmm22_prm)
assert os.path.isfile(fn_charmm22_psf)
assert os.path.isfile(fn_sys)
# Count the number of BOND, ANGLES and DIHEDRAL lines in the PRM file.
counts = {}
with open(fn_charmm22_prm, 'r') as f:
for line in f:
print line
line = line[:line.find('!')].strip()
if len(line) == 0:
continue
if line in ['BONDS','ANGLES', 'DIHEDRALS', 'IMPROPER']:
key = line
counts[key] = 0
else:
counts[key] += 1
assert counts['BONDS'] == 4
assert counts['ANGLES'] == 5
assert counts['DIHEDRALS'] == 2
assert counts['IMPROPER'] == 0
# Count the number atoms, bonds, angles and dihedrals in the PSF file and
# check for consistency.
with open(fn_charmm22_psf, 'r') as f:
natom = 0
assert f.next() == 'PSF\n'
for line in f:
if '!NATOM' in line:
natom = int(line.split()[0])
break
assert natom == system.natom
for iatom in xrange(natom+1):
f.next()
line = f.next()
assert '!NBOND: bonds' in line
nbond = int(line.split()[0])
nline = int(np.ceil(nbond/4.0))
numbers = (''.join([f.next() for iline in xrange(nline)])).split()
assert len(numbers) == nbond*2
f.next()
line = f.next()
assert '!NTHETA: angles' in line
ntheta = int(line.split()[0])
nline = int(np.ceil(ntheta/3.0))
numbers = (''.join([f.next() for iline in xrange(nline)])).split()
assert len(numbers) == ntheta*3
f.next()
line = f.next()
assert '!NPHI: dihedrals' in line
nphi = int(line.split()[0])
nline = int(np.ceil(nphi/2.0))
numbers = (''.join([f.next() for iline in xrange(nline)])).split()
assert len(numbers) == nphi*4
f.next()
line = f.next()
assert '!NIMPHI: impropers' in line
nimphi = int(line.split()[0])
assert nimphi == 0
def run(runcycle, indb, outdb):
progname = common.progname()
logfile1 = common.tmpdir() + "/copy" + str(runcycle) + ".log"
logfile2 = common.tmpdir() + "/validate" + str(runcycle) + ".log"
if not os.path.exists(indb):
print "{0}: Input database {1} does not exist".format(progname, indb)
return False
if os.path.exists(logfile1):
os.remove(logfile1)
if os.path.exists(logfile2):
os.remove(logfile2)
if os.path.exists(outdb):
os.remove(outdb)
print "========================================================================================"
print "{0}: Copying {1} to {2}".format(progname, indb, outdb)
cmdline = common.ccore()
cmdline += " -l {0} -i {1} -o {2} --quiet=true --debuglog=true copydb".format(logfile1, indb, outdb)
if not common.runccore(cmdline):
return False
common.checkLogfile(logfile1)
# Check that the copy was successful
found = False
f = open(logfile1, "r")
for line in f:
if re.search("Successfully copied database", line):
found = True
break
if found:
print "{0}: Copy successful".format(progname)
else:
print "{0}: Copy failed".format(progname)
return False
print "----------------------------------------------------------------------------------------"
print "{0}: Validating {1}".format(progname, outdb)
cmdline = common.ccore()
cmdline += " -l {0} -i {1} --quiet true --debuglog true validatedb".format(logfile2, outdb)
if not common.runccore(cmdline):
return False
common.checkLogfile(logfile2)
# Check that the validate was successful
found = False
f = open(logfile2, "r")
for line in f:
if re.search("Database is valid", line):
found = True
break
if found:
print "{0}: Validate successful".format(progname)
else:
print "{0}: Validate failed".format(progname)
return False
return True
def test_output_charmm22():
with log.section('NOSETST', 2):
system, ai = read_system('ethanol/gaussian.fchk')
set_ffatypes(system, 'low')
with tmpdir('test_output_charmm22') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_charmm22_prm = os.path.join(dn, 'test.prm')
fn_charmm22_psf = os.path.join(dn, 'test.psf')
fn_sys = os.path.join(dn, 'system.chk')
settings = Settings(
do_cross_ASS=False, do_cross_ASA=False,
fn_yaff=fn_yaff, fn_sys=fn_sys,
fn_charmm22_prm=fn_charmm22_prm,
fn_charmm22_psf=fn_charmm22_psf,
)
program = DeriveFF(system, ai, settings)
program.run()
assert os.path.isfile(fn_yaff)
assert os.path.isfile(fn_charmm22_prm)
assert os.path.isfile(fn_charmm22_psf)
assert os.path.isfile(fn_sys)
# Count the number of BOND, ANGLES and DIHEDRAL lines in the PRM file.
counts = {}
with open(fn_charmm22_prm, 'r') as f:
for line in f:
print(line)
line = line[:line.find('!')].strip()
if len(line) == 0:
continue
if line in ['BONDS','ANGLES', 'DIHEDRALS', 'IMPROPER']:
key = line
counts[key] = 0
else:
counts[key] += 1
assert counts['BONDS'] == 4
assert counts['ANGLES'] == 5
assert counts['DIHEDRALS'] == 3
assert counts['IMPROPER'] == 0
# Count the number atoms, bonds, angles and dihedrals in the PSF file and
# check for consistency.
with open(fn_charmm22_psf, 'r') as f:
natom = 0
assert next(f) == 'PSF\n'
for line in f:
if '!NATOM' in line:
natom = int(line.split()[0])
break
assert natom == system.natom
for iatom in range(natom+1):
next(f)
line = next(f)
assert '!NBOND: bonds' in line
nbond = int(line.split()[0])
nline = int(np.ceil(nbond/4.0))
numbers = (''.join([next(f) for iline in range(nline)])).split()
assert len(numbers) == nbond*2
next(f)
line = next(f)
assert '!NTHETA: angles' in line
ntheta = int(line.split()[0])
nline = int(np.ceil(ntheta/3.0))
numbers = (''.join([next(f) for iline in range(nline)])).split()
assert len(numbers) == ntheta*3
next(f)
line = next(f)
assert '!NPHI: dihedrals' in line
nphi = int(line.split()[0])
nline = int(np.ceil(nphi/2.0))
numbers = (''.join([next(f) for iline in range(nline)])).split()
assert len(numbers) == nphi*4
next(f)
line = next(f)
assert '!NIMPHI: impropers' in line
nimphi = int(line.split()[0])
assert nimphi == 0
