def func(x):
modtype = 'Constrained_DM'
params = [0., 1., 2., 3., 4., r, x]
options = ["lj"]
condm = rp.ModHam(nalpha,
nalpha,
norb,
modtype,
options,
params,
matrixelements=matrixelements)
condm.write_file(fname='conelements.mod')
ht.create_ciflow_input_file('conelements.mod',
methods,
fname=flowname)
ci_flow = ""
if methods:
try:
ci_flow = ""
process = subprocess.Popen(["./ciflow_%s.x" % pokemon],
stdin=open(flowname, 'r'),
stdout=subprocess.PIPE)
for line in iter(process.stdout.readline, ''):
sys.stdout.write(
line) #writes intermediate output to screen.
outputfile.write(line)
outputfile.flush()
ci_flow += line
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
print ci_flow
energies = ht.process_output(ci_flow)
mullikencharge = float(
re.search(
"Mulliken[\s\w]+:\s*([\-+]?\d+[\.,]?\d*[eEDd]?[\-+]?\d*)",
ci_flow).group(1))
return (energies, mullikencharge)
def func(x):
modtype = 'Constrained_DM' ; params = [0. , 1. , 2. , 3. , 4. , r , x] ; options = [ "lj"]
condm = rp.ModHam(nalpha, nalpha,norb,modtype , options , params, matrixelements =matrixelements)
condm.write_file(fname = 'conelements.mod')
ht.create_ciflow_input_file('conelements.mod', methods , fname = flowname)
ci_flow =""
if methods:
try:
ci_flow =""
process = subprocess.Popen(["./ciflow_%s.x" %pokemon] , stdin =open(flowname , 'r'), stdout = subprocess.PIPE)
for line in iter(process.stdout.readline, ''):
sys.stdout.write(line) #writes intermediate output to screen.
outputfile.write(line)
outputfile.flush()
ci_flow += line
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
print ci_flow
energies = ht.process_output(ci_flow)
mullikencharge = float(re.search("Mulliken[\s\w]+:\s*([\-+]?\d+[\.,]?\d*[eEDd]?[\-+]?\d*)", ci_flow).group(1) )
return (energies , mullikencharge)
def hub1d():
pokemon = os.environ['VSC_INSTITUTE_CLUSTER']
flowname = "flow.dat"
psienergies = []
methods = ["fci", "none"]
nalpha = 4
norb = 8
options = ['notzero', 'pos', 'per']
name = 'hub1dmpdnorb' + str(norb) + 'pair' + str(nalpha) + options[
2] + 'U0-100' #relative to the directory that contains this script
import numpy as np
runlist = range(0, 101)
runlist = [0.1, 1, 4, 10, 100]
modtype = 'Hub1d'
params = [1., 4.]
arrayid = 2
#hereunder for array jobs for heavy calculations. But make sure it is always defined
#arrayid =int(os.getenv('PBS_ARRAYID'))
#arraystep = 1
#name += str(arrayid)
#try:
# runlist = runlist[(arrayid-1) * arraystep : arrayid *arraystep]
#except:
# print 'encoutered exception in cut of runlist.'
# runlist = runlist[-4:-1]
print 'Start to load necessary modules.'
os.system('module load cluster/%s' % pokemon)
os.system('module load PSI/4.0b6-20160201-intel-2016a-mt-Python-2.7.11')
os.system('module load arpack-ng/3.3.0-intel-2016a')
os.system('module load OpenBabel/2.3.2-intel-2014b-Python-2.7.8')
os.system('module load matplotlib')
os.system('module load h5py')
#os.system('module load Boost/1.55.0-ictce-7.1.2-Python-2.7.8')
os.system('export MKL_NUM_THREADS=16')
#os.system('export KMP_STACKSIZE=32m')
ORIGDIR = os.getenv('HOME')
mofile = os.path.join(ORIGDIR,
'devel/CIFlow/lib/mointegrals_%s.so' % pokemon)
exefile = os.path.join(ORIGDIR, 'devel/CIFlow/bin/ciflow_%s.x' % pokemon)
#hamdir = os.path.join(ORIGDIR, hamdirname)
#det_file = os.path.join(ORIGDIR, detfile10 )
print 'We submitted the script in: ', ORIGDIR
print 'Psi 4 plugin is at: ', mofile
WORKDIR = os.path.join(os.getenv('VSC_SCRATCH_NODE'),
os.getenv('PBS_JOBID'))
if os.path.isdir(WORKDIR):
shutil.rmtree(WORKDIR)
os.mkdir(WORKDIR)
print 'Workdir is: ', WORKDIR
shutil.copy(mofile, WORKDIR)
shutil.copy(exefile, WORKDIR)
#hamdest = os.path.join(WORKDIR, hamdirname)
#shutil.copytree(hamdir,hamdest)
#shutil.move(det_file,WORKDIR)
os.chdir(WORKDIR)
print 'We work on node: ', os.getenv('HOSTNAME')
create_modham_input(nalpha, norb, modtype, options, params, runlist)
fileinfo = lambda x: float(
re.search(r'run[-\w\d=]*([\-+]?\d+[\.,]?\d*[eEDd]?[\-+]?\d*)\.mod', x).
group(1))
search = modtype + '.+mod'
hamfiles = File_Collector(
'.',
search=search,
notsearch=r'\.sw\w',
sortfunction=fileinfo,
filterf=lambda x: fileinfo(x) >= -1 and fileinfo(x) < 1000.)
print 'Contents of rundir before run are: ', os.listdir(os.getcwd())
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[[], [1]], [] , fname = detfile3 ,add_frozen = 0, ref = [lambda x , y , z : psir.get_hf_orbs()]) #CIS(P)
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[[], [1,2]], [] , fname = detfile4 ,add_frozen = 0, ref = [lambda x , y , z : psir.get_hf_orbs()]) #CISD(P)
afh = 'R'
fname = "ciflowresults.dat"
with open(fname, 'w') as f:
header = ht.create_header(afh, methods, psienergies)
print header
f.write(header)
for index, matrixelements in enumerate(hamfiles.plotfiles):
ht.create_ciflow_input_file(matrixelements,
methods,
fname=flowname)
ci_flow = ""
try:
process = subprocess.Popen(["./ciflow_%s.x" % pokemon],
stdin=open(flowname, 'r'),
stdout=subprocess.PIPE)
for line in iter(process.stdout.readline, ''):
sys.stdout.write(line)
ci_flow += line
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
"""
try:
ci_flow = subprocess.check_output(['./ciflow_%s.x' %pokemon ] , stdin =open(flowname , 'r') )
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
"""
energies = ht.process_output(ci_flow)
ht.print_output(matrixelements, energies, methods)
f.write("%.15f\t%s\n" % (runlist[index], '\t'.join(energies)))
os.remove('./ciflow_%s.x' % pokemon)
os.remove('./mointegrals.so')
#os.remove(detfile1)
ht.generate_dir('output_files', None, prefix=r'output[\w_]+.dat')
os.chdir('..')
ht.generate_dir('unitaries', None, prefix='unitary_')
os.chdir('..')
ht.generate_dir('matrixelements_otherbasis', None, prefix='hamp')
os.chdir('..')
OUTPUTDIR = os.path.join(ORIGDIR, name + str(arrayid))
print 'We Start to create the outputdir ', OUTPUTDIR
if os.path.isdir(OUTPUTDIR):
shutil.rmtree(OUTPUTDIR)
make_tarfile(OUTPUTDIR, WORKDIR)
DATADIR = os.path.join(os.getenv('VSC_DATA'),
name + str(arrayid) + os.getenv('PBS_JOBID'))
make_tarfile(DATADIR, WORKDIR)
print 'We made a copy of the jobdata to: ', DATADIR
def main():
name = 'beh2cc-pvdzcisddocidebug'
hamdirname = "beh2ccpvdzham"
pokemon = os.environ['VSC_INSTITUTE_CLUSTER']
print 'we have run this script on cluster: ', pokemon
active_space = False
flowname = "flow.dat"
detfile1 = "cisddeterminants.dat"
detfile2 = "cisddocideterminants.dat"
detfile3 = 'CIS(P)'
detfile4 = 'CISD(P)'
detfile6 = 'fcifile.dat'
detfile7 = 'be_ccpv5z96100.txt'
detfile10 = "linhyb23p.dat"
detfile11 = "linhyb2p.dat"
#methods = [ "big", detfile6, "loadham"] #everything on#everything on
methods = ["file", detfile1, "hmmin", "file", detfile10,
"loadham"] #everything on#everything on
methods = [
"doci", "loadham", "file", detfile3, "loadham", "file", detfile4,
"loadham"
] #everything on#everything on
#methods = []
#psienergies = ['fci']
psienergies = []
basissets = ['cc-pvdz']
#runlist = [ 3.4 , 3.5 , 3.8 , 3.9 , 4. , 4.5 ,4.8 , 5., 5.6, 6.] #BeH2 (linear)
#runlist = [1.81625952410, 1.97501269880, 2.13376587350, 2.29251904820, 2.45127222290, 2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 4. , 4.5 , 5.] #BeH2
runlist = [
0.7, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.81625952410,
1.97501269880, 2.13376587350, 2.29251904820, 2.45127222290,
2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170, 3.1, 3.2,
3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4., 4.5, 5., 6.
] #BeH2
#runlist = [0.6402695456, 0.7 , 0.7461049954, 0.8 , 0.8519404452, 0.9 , 0.957775895, 1. , 1.0636113448, 1.1, 1.1694467946, 1.2 , 1.2752822444, 1.3, 1.3811176942, 1.4, 1.486953144, 1.5, 1.5927885938, 1.6, 1.6986240436 , 1.72 , 1.8 , 1.85 , 1.9 , 1.95 , 2. , 2.05, 2.2278012926, 2.4 , 2.6 , 3. , 3.5 , 4. , 4.5 , 5. ,6.]#, 2.1 , 2.15, 2.2278012926 ]#, 1.8044594934, 1.9102949432, 2.016130393, 2.1219658428, 2.2278012926, 2.3336367424 ] #H2O (c2v)
#runlist = [2.3,2.4,2.5,2.6,2.7,2.8,2.9,3.,3.2,3.3, 3.5,3.8 , 4.]
#runlist = [2.32,2.42,2.52,2.61,2.71,2.99,3.09,3.19,3.38,3.57, 3.76,4.05]
#runlist = [1.9] + runlist
#runlist = [1.81625952410, 1.97501269880, 2.13376587350, 2.29251904820, 2.45127222290, 2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 4. , 4.5 , 5.] #BeH2
#runlist = [2.45127222290, 2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 4. , 4.5 , 5.] #BeH2
#runlist = []
arrayid = 2
#hereunder for array jobs for heavy calculations. But make sure it is always defined
#arrayid =int(os.getenv('PBS_ARRAYID'))
#arraystep = 1
#name += str(arrayid)
#try:
# runlist = runlist[(arrayid-1) * arraystep : arrayid *arraystep]
#except:
# print 'encoutered exception in cut of runlist.'
# runlist = runlist[-4:-1]
#runlist = [1.38, 1.4, 1.45, 1.5, 1.65750634940, 1.81625952410, 1.97501269880] #, 2.13376587350,2.2 , 2.29251904820, 2.35 , 2.45127222290, 2.5 , 2.61002539760,2.7 , 2.76877857230, 2.92753174700, 3.0 , 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 3.6 ,3.7 , 3.8 , 3.9 , 4. , 4.5 , 5. , 6.] #BeH2 (linear)
#runlist = [2.13376587350,2.2 , 2.29251904820, 2.35 , 2.45127222290, 2.5 ]# , 2.61002539760,2.7 , 2.76877857230, 2.92753174700, 3.0 , 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 3.6 ,3.7 , 3.8 , 3.9 , 4. , 4.5 , 5. , 6.] #BeH2 (linear)
#runlist = [ 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 4. , 5. , 6.] #BeH2 (linear)
#runlist = [0.86374047590, 1.02249365060, 1.18124682530, 1.34000000000, 1.49875317470, 1.65750634940, 1.81625952410, 1.97501269880, 2.13376587350, 2.29251904820, 2.45127222290, 2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170 ] #BeH2
#runlist = [0.6402695456, 0.7461049954, 0.8519404452, 0.957775895, 1.0636113448, 1.1694467946, 1.2752822444, 1.3811176942, 1.486953144, 1.5927885938, 1.6986240436 , 2.2278012926 ]#, 1.8044594934, 1.9102949432, 2.016130393, 2.1219658428, 2.2278012926, 2.3336367424 ] #H2O
#runlist = [ 1.2 , 1.6] #[ 0.7,0.8 ,0.8519404452, 0.957775895, 1.1694467946, 1.2752822444, 1.3811176942]#, 1.8044594934, 1.9102949432, 2.016130393, 2.1219658428, 2.2278012926, 2.3336367424 ] #H2O
#runlist = [0.848, 0.9 , 0.973, 1.0 , 1.098, 1.223, 1.3, 1.348, 1.4, 1.473,1.5, 1.598, 1.723,1.8 , 1.848, 1.973] #N2
#atoms = [7,7] # set DOCC = [3, 0 ,0, 0,0 , 2, 1 ,1]
#atoms = [1, 1,1,1,1,1,1,1 ] #h8
#atoms = [8, 1,1 ]
atoms = [4, 1, 1]
#atoms = [6,6,6,6,6,6,1,1,1,1,1,1] #benzene
#import math
#runlist = [x*math.pi/180. for x in range(55,60) + [59.9 , 60] ] #angle between two triangles in benzene.
print 'Start to load necessary modules.'
os.system('module swap cluster/%s' % pokemon)
os.system('module load PSI/4.0b6-20160201-intel-2016a-mt-Python-2.7.11')
os.system('module load arpack-ng/3.3.0-intel-2016a')
os.system('module load matplotlib')
os.system('module load h5py')
#os.system('module load Boost/1.55.0-ictce-7.1.2-Python-2.7.8')
os.system('export MKL_NUM_THREADS=16')
#os.system('export KMP_STACKSIZE=32m')
ORIGDIR = os.getenv('HOME')
mofile = os.path.join(ORIGDIR,
'devel/CIFlow/lib/mointegrals_%s.so' % pokemon)
exefile = os.path.join(ORIGDIR, 'devel/CIFlow/bin/ciflow_%s.x' % pokemon)
hamdir = os.path.join(ORIGDIR, hamdirname)
#det_file = os.path.join(ORIGDIR, detfile10 )
print 'We submitted the script in: ', ORIGDIR
print 'Psi 4 plugin is at: ', mofile
WORKDIR = os.path.join(os.getenv('VSC_SCRATCH_NODE'),
os.getenv('PBS_JOBID'))
if os.path.isdir(WORKDIR):
shutil.rmtree(WORKDIR)
os.mkdir(WORKDIR)
print 'Workdir is: ', WORKDIR
shutil.copy(mofile, WORKDIR)
shutil.copy(exefile, WORKDIR)
hamdest = os.path.join(WORKDIR, hamdirname)
shutil.copytree(hamdir, hamdest)
#shutil.move(det_file,WORKDIR)
os.chdir(WORKDIR)
print 'We work on node: ', os.getenv('HOSTNAME')
#PSIINPUT = os.path.join(os.getcwd() , 'output_run')
#print 'We Start to create the outputdir ' ,PSIINPUT
#if os.path.isdir(PSIINPUT):
# shutil.rmtree(PSIINPUT)
#os.mkdir(PSIINPUT)
#angle = 104.479848
#for basis in basissets:
# for r in runlist:
# #positions = [[0,0,0],[0,0,r],[0,0,-1*r]] #for molecules like beh2
# #positions = [[0,0,0],[0,0,r]] #for molecules like n2
# #positions = [[0,0,0],[0,0,r],[0,0,2*r], [0,0,3*r], [0,0,4*r] , [0,0,5*r] , [0,0,6*r], [0,0,7*r]] #For H_8
# positions = [[''],[1, r],[1, r, 2 , angle]] #for molecules like h2o
# #positions = [[0,0,0]] #for an atom
# #positions = ht.benzene(r, 1.398) #REMARK we run over the angle -> r in runlist, and keep the radius of the circle on which all the C atoms are placed constant to extrapar, (extrapar = 1.398 A is standard)
# ht.input_psi(os.path.join('output_run' ,"psi%.2f" %(r) +"basis"+basis+ ".dat"), basis ,name= 'mol' , charge_mult = (0,1) , atomlist = atoms , positions = positions , units = 'angstrom' , ref = 'rhf', userbasis = False, path_to_plugin = './mointegrals_%s.so' %pokemon, DOCC = None, sym = None, energies = psienergies)
print 'Contents of rundir before run are: ', os.listdir(os.getcwd())
#for file in os.listdir(PSIINPUT):
# print 'processing psi input file: ' , file
# exfile = os.path.join('output_run',file)
# os.system('psi4 ' + exfile)
#print 'Contents of rundir after run are: ', os.listdir(os.getcwd())
#print 'Contents of inputdir are: ', os.listdir('./output_run')
hamfiles = File_Collector(
'.',
search=r'psi.+out',
notsearch=r'\.sw\w',
sortfunction=lambda x: float(
re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?).*\.m?out', x).group(1)),
filterf=lambda x: (float(
re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*).*\.m?out', x).
group(1)) == round(runlist[arrayid], 2)))
#hamfiles =File_Collector('output_run', search = r'psi.+out' ,notsearch = r'\.sw\w', filterf = lambda x: float(re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*).*\.m?out' , x).group(1)) > 1.1)
psir = rp.PsiReader(hamfiles.plotfiles[0],
isbig=False,
numorbs=-1,
read_ints=False)
#frozen = [1,0,0,0,0,1,0,0] ; virtual = [1,1,1,1,1,2,0,0]; active = [5,0,2,2,0,4,3,3]
#assert( sum(frozen) + sum(virtual) + sum(active) == psir.values['norb'])
#dw.cimain(psir.values['nalpha'] - sum(frozen),psir.values['nbeta'] -sum(frozen) ,psir.values['norb'] - sum(frozen) - sum(virtual) , [[1,2], []], [],fname = detfile1 ,ref = [lambda x , y , z : psir.get_hf_orbs( frozen = frozen , virtual = virtual )] , active = active, frozen = frozen, virtual = virtual ,add_frozen = 0, add_virtual = 0)
#dw.cimain(psir.values['nalpha'] - sum(frozen),psir.values['nbeta'] -sum(frozen) ,psir.values['norb'] - sum(frozen) - sum(virtual) , [[1,2], [2,3]], [],fname = detfile10 ,ref = [lambda x , y , z : psir.get_hf_orbs( frozen = frozen , virtual = virtual )] , active = active, frozen = frozen, virtual = virtual ,add_frozen = 0, add_virtual = 0)
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'] , [[1,2],[2]], [] , fname = detfile11 ,add_frozen = 0, add_virtual = 0,ref = [ lambda x , y , z : psir.get_hf_orbs()] ) #CISDD
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'] , [[1,2],[]], [0] , fname = detfile2 ,add_frozen = 0, add_virtual = 0,ref = [ lambda x , y , z : psir.get_hf_orbs()] ) #CISDDOCI
dw.cimain(psir.values['nalpha'],
psir.values['nbeta'],
psir.values['norb'], [[], [1]], [],
fname=detfile3,
add_frozen=0,
ref=[lambda x, y, z: psir.get_hf_orbs()]) #CIS(P)
dw.cimain(psir.values['nalpha'],
psir.values['nbeta'],
psir.values['norb'], [[], [1, 2]], [],
fname=detfile4,
add_frozen=0,
ref=[lambda x, y, z: psir.get_hf_orbs()]) #CISD(P)
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[[1,2], [] ],[] , fname = detfile1 ,add_frozen = 0, ref = [lambda x , y , z : psir.get_hf_orbs()]) #CISD
#dw.cimain(psir.values['nalpha']-1,psir.values['nbeta']-1, psir.values['norb']-1,[[1,2,3,4], [] ],[] , fname = detfile6 ,add_frozen = 1, ref = [lambda x , y , z : dw.get_hf_det(x,y,z)] ) #FCI
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[range(1,psir.values['nbeta']*2 +1), [] ],[] , fname = detfile6 ,add_frozen = 0, ref = [lambda x , y , z : dw.get_hf_det(x,y,z)] ) #FCI
afh = 'R'
for basis in basissets:
fname = "ciflowresults_" + basis + ".dat"
with open(fname, 'w') as f:
header = ht.create_header(afh, methods, psienergies)
print header
f.write(header)
for index, matrixelements in enumerate(hamfiles.plotfiles):
psir = rp.PsiReader(matrixelements,
isbig=False,
numorbs=-1,
read_ints=False)
if active_space:
psir.set_active_space(
[0], [[1, 2], []], [],
detfile1) #for pisystem of deformed benzene
psir.set_active_space(
[0], [[1, 2], [2]], [],
detfile11) #for pisystem of deformed benzene
ht.create_ciflow_input_file(matrixelements,
methods,
fname=flowname)
ci_flow = ""
try:
process = subprocess.Popen(["./ciflow_%s.x" % pokemon],
stdin=open(flowname, 'r'),
stdout=subprocess.PIPE)
for line in iter(process.stdout.readline, ''):
sys.stdout.write(line)
ci_flow += line
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
"""
try:
ci_flow = subprocess.check_output(['./ciflow_%s.x' %pokemon ] , stdin =open(flowname , 'r') )
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
"""
energies = ht.process_output(ci_flow) + [
x[1] for x in psir.extract_energies()
]
ht.print_output(matrixelements, energies, methods)
f.write("%.15f\t%s\n" % (runlist[index], '\t'.join(energies)))
os.remove('./ciflow_%s.x' % pokemon)
os.remove('./mointegrals.so')
#os.remove(detfile1)
ht.generate_dir('output_files', None, prefix=r'output[\w_]+.dat')
os.chdir('..')
ht.generate_dir('unitaries', None, prefix='unitary_')
os.chdir('..')
ht.generate_dir('matrixelements_otherbasis', None, prefix='hamp')
os.chdir('..')
OUTPUTDIR = os.path.join(ORIGDIR, name + str(arrayid))
print 'We Start to create the outputdir ', OUTPUTDIR
if os.path.isdir(OUTPUTDIR):
shutil.rmtree(OUTPUTDIR)
make_tarfile(OUTPUTDIR, WORKDIR)
DATADIR = os.path.join(os.getenv('VSC_DATA'),
name + str(arrayid) + os.getenv('PBS_JOBID'))
make_tarfile(DATADIR, WORKDIR)
print 'We made a copy of the jobdata to: ', DATADIR
def main():
name = 'beh2cc-pvdzcisddocidebug'
hamdirname = "beh2ccpvdzham"
pokemon = os.environ['VSC_INSTITUTE_CLUSTER']
print 'we have run this script on cluster: ' , pokemon
active_space = False
flowname = "flow.dat"; detfile1 = "cisddeterminants.dat" ; detfile2 = "cisddocideterminants.dat" ; detfile3 = 'CIS(P)' ; detfile4 = 'CISD(P)' ; detfile6 = 'fcifile.dat' ; detfile7 = 'be_ccpv5z96100.txt'
detfile10= "linhyb23p.dat"
detfile11 = "linhyb2p.dat"
#methods = [ "big", detfile6, "loadham"] #everything on#everything on
methods = [ "file" , detfile1 , "hmmin", "file" ,detfile10 , "loadham"] #everything on#everything on
methods = ["doci" , "loadham" , "file", detfile3 , "loadham" , "file" , detfile4 , "loadham" ] #everything on#everything on
#methods = []
#psienergies = ['fci']
psienergies = []
basissets = ['cc-pvdz']
#runlist = [ 3.4 , 3.5 , 3.8 , 3.9 , 4. , 4.5 ,4.8 , 5., 5.6, 6.] #BeH2 (linear)
#runlist = [1.81625952410, 1.97501269880, 2.13376587350, 2.29251904820, 2.45127222290, 2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 4. , 4.5 , 5.] #BeH2
runlist = [0.7, 0.9 , 1, 1.1 , 1.2 , 1.3 ,1.4 , 1.5 , 1.6 , 1.7, 1.81625952410, 1.97501269880, 2.13376587350, 2.29251904820, 2.45127222290, 2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 ,3.6,3.7,3.8,3.9 , 4. , 4.5 , 5., 6.] #BeH2
#runlist = [0.6402695456, 0.7 , 0.7461049954, 0.8 , 0.8519404452, 0.9 , 0.957775895, 1. , 1.0636113448, 1.1, 1.1694467946, 1.2 , 1.2752822444, 1.3, 1.3811176942, 1.4, 1.486953144, 1.5, 1.5927885938, 1.6, 1.6986240436 , 1.72 , 1.8 , 1.85 , 1.9 , 1.95 , 2. , 2.05, 2.2278012926, 2.4 , 2.6 , 3. , 3.5 , 4. , 4.5 , 5. ,6.]#, 2.1 , 2.15, 2.2278012926 ]#, 1.8044594934, 1.9102949432, 2.016130393, 2.1219658428, 2.2278012926, 2.3336367424 ] #H2O (c2v)
#runlist = [2.3,2.4,2.5,2.6,2.7,2.8,2.9,3.,3.2,3.3, 3.5,3.8 , 4.]
#runlist = [2.32,2.42,2.52,2.61,2.71,2.99,3.09,3.19,3.38,3.57, 3.76,4.05]
#runlist = [1.9] + runlist
#runlist = [1.81625952410, 1.97501269880, 2.13376587350, 2.29251904820, 2.45127222290, 2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 4. , 4.5 , 5.] #BeH2
#runlist = [2.45127222290, 2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 4. , 4.5 , 5.] #BeH2
#runlist = []
arrayid = 2
#hereunder for array jobs for heavy calculations. But make sure it is always defined
#arrayid =int(os.getenv('PBS_ARRAYID'))
#arraystep = 1
#name += str(arrayid)
#try:
# runlist = runlist[(arrayid-1) * arraystep : arrayid *arraystep]
#except:
# print 'encoutered exception in cut of runlist.'
# runlist = runlist[-4:-1]
#runlist = [1.38, 1.4, 1.45, 1.5, 1.65750634940, 1.81625952410, 1.97501269880] #, 2.13376587350,2.2 , 2.29251904820, 2.35 , 2.45127222290, 2.5 , 2.61002539760,2.7 , 2.76877857230, 2.92753174700, 3.0 , 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 3.6 ,3.7 , 3.8 , 3.9 , 4. , 4.5 , 5. , 6.] #BeH2 (linear)
#runlist = [2.13376587350,2.2 , 2.29251904820, 2.35 , 2.45127222290, 2.5 ]# , 2.61002539760,2.7 , 2.76877857230, 2.92753174700, 3.0 , 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 3.5 , 3.6 ,3.7 , 3.8 , 3.9 , 4. , 4.5 , 5. , 6.] #BeH2 (linear)
#runlist = [ 3.08628492170, 3.1 , 3.2, 3.3 , 3.4 , 4. , 5. , 6.] #BeH2 (linear)
#runlist = [0.86374047590, 1.02249365060, 1.18124682530, 1.34000000000, 1.49875317470, 1.65750634940, 1.81625952410, 1.97501269880, 2.13376587350, 2.29251904820, 2.45127222290, 2.61002539760, 2.76877857230, 2.92753174700, 3.08628492170 ] #BeH2
#runlist = [0.6402695456, 0.7461049954, 0.8519404452, 0.957775895, 1.0636113448, 1.1694467946, 1.2752822444, 1.3811176942, 1.486953144, 1.5927885938, 1.6986240436 , 2.2278012926 ]#, 1.8044594934, 1.9102949432, 2.016130393, 2.1219658428, 2.2278012926, 2.3336367424 ] #H2O
#runlist = [ 1.2 , 1.6] #[ 0.7,0.8 ,0.8519404452, 0.957775895, 1.1694467946, 1.2752822444, 1.3811176942]#, 1.8044594934, 1.9102949432, 2.016130393, 2.1219658428, 2.2278012926, 2.3336367424 ] #H2O
#runlist = [0.848, 0.9 , 0.973, 1.0 , 1.098, 1.223, 1.3, 1.348, 1.4, 1.473,1.5, 1.598, 1.723,1.8 , 1.848, 1.973] #N2
#atoms = [7,7] # set DOCC = [3, 0 ,0, 0,0 , 2, 1 ,1]
#atoms = [1, 1,1,1,1,1,1,1 ] #h8
#atoms = [8, 1,1 ]
atoms = [4,1,1]
#atoms = [6,6,6,6,6,6,1,1,1,1,1,1] #benzene
#import math
#runlist = [x*math.pi/180. for x in range(55,60) + [59.9 , 60] ] #angle between two triangles in benzene.
print 'Start to load necessary modules.'
os.system('module swap cluster/%s' %pokemon)
os.system('module load PSI/4.0b6-20160201-intel-2016a-mt-Python-2.7.11')
os.system('module load arpack-ng/3.3.0-intel-2016a')
os.system('module load matplotlib')
os.system('module load h5py')
#os.system('module load Boost/1.55.0-ictce-7.1.2-Python-2.7.8')
os.system('export MKL_NUM_THREADS=16')
#os.system('export KMP_STACKSIZE=32m')
ORIGDIR= os.getenv('HOME')
mofile = os.path.join(ORIGDIR, 'devel/CIFlow/lib/mointegrals_%s.so' %pokemon)
exefile = os.path.join(ORIGDIR, 'devel/CIFlow/bin/ciflow_%s.x' %pokemon )
hamdir = os.path.join(ORIGDIR, hamdirname)
#det_file = os.path.join(ORIGDIR, detfile10 )
print 'We submitted the script in: ', ORIGDIR
print 'Psi 4 plugin is at: ' , mofile
WORKDIR= os.path.join(os.getenv('VSC_SCRATCH_NODE'),os.getenv('PBS_JOBID'))
if os.path.isdir(WORKDIR):
shutil.rmtree(WORKDIR)
os.mkdir(WORKDIR)
print 'Workdir is: ', WORKDIR
shutil.copy(mofile,WORKDIR)
shutil.copy(exefile,WORKDIR)
hamdest = os.path.join(WORKDIR, hamdirname)
shutil.copytree(hamdir,hamdest)
#shutil.move(det_file,WORKDIR)
os.chdir(WORKDIR)
print 'We work on node: ' , os.getenv('HOSTNAME')
#PSIINPUT = os.path.join(os.getcwd() , 'output_run')
#print 'We Start to create the outputdir ' ,PSIINPUT
#if os.path.isdir(PSIINPUT):
# shutil.rmtree(PSIINPUT)
#os.mkdir(PSIINPUT)
#angle = 104.479848
#for basis in basissets:
# for r in runlist:
# #positions = [[0,0,0],[0,0,r],[0,0,-1*r]] #for molecules like beh2
# #positions = [[0,0,0],[0,0,r]] #for molecules like n2
# #positions = [[0,0,0],[0,0,r],[0,0,2*r], [0,0,3*r], [0,0,4*r] , [0,0,5*r] , [0,0,6*r], [0,0,7*r]] #For H_8
# positions = [[''],[1, r],[1, r, 2 , angle]] #for molecules like h2o
# #positions = [[0,0,0]] #for an atom
# #positions = ht.benzene(r, 1.398) #REMARK we run over the angle -> r in runlist, and keep the radius of the circle on which all the C atoms are placed constant to extrapar, (extrapar = 1.398 A is standard)
# ht.input_psi(os.path.join('output_run' ,"psi%.2f" %(r) +"basis"+basis+ ".dat"), basis ,name= 'mol' , charge_mult = (0,1) , atomlist = atoms , positions = positions , units = 'angstrom' , ref = 'rhf', userbasis = False, path_to_plugin = './mointegrals_%s.so' %pokemon, DOCC = None, sym = None, energies = psienergies)
print 'Contents of rundir before run are: ', os.listdir(os.getcwd())
#for file in os.listdir(PSIINPUT):
# print 'processing psi input file: ' , file
# exfile = os.path.join('output_run',file)
# os.system('psi4 ' + exfile)
#print 'Contents of rundir after run are: ', os.listdir(os.getcwd())
#print 'Contents of inputdir are: ', os.listdir('./output_run')
hamfiles = File_Collector('.', search = r'psi.+out' ,notsearch = r'\.sw\w',sortfunction = lambda x: float(re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?).*\.m?out' , x).group(1)) , filterf = lambda x: (float(re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*).*\.m?out' , x).group(1)) == round(runlist[arrayid],2 ) ) )
#hamfiles =File_Collector('output_run', search = r'psi.+out' ,notsearch = r'\.sw\w', filterf = lambda x: float(re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*).*\.m?out' , x).group(1)) > 1.1)
psir = rp.PsiReader(hamfiles.plotfiles[0], isbig = False, numorbs = -1 , read_ints = False)
#frozen = [1,0,0,0,0,1,0,0] ; virtual = [1,1,1,1,1,2,0,0]; active = [5,0,2,2,0,4,3,3]
#assert( sum(frozen) + sum(virtual) + sum(active) == psir.values['norb'])
#dw.cimain(psir.values['nalpha'] - sum(frozen),psir.values['nbeta'] -sum(frozen) ,psir.values['norb'] - sum(frozen) - sum(virtual) , [[1,2], []], [],fname = detfile1 ,ref = [lambda x , y , z : psir.get_hf_orbs( frozen = frozen , virtual = virtual )] , active = active, frozen = frozen, virtual = virtual ,add_frozen = 0, add_virtual = 0)
#dw.cimain(psir.values['nalpha'] - sum(frozen),psir.values['nbeta'] -sum(frozen) ,psir.values['norb'] - sum(frozen) - sum(virtual) , [[1,2], [2,3]], [],fname = detfile10 ,ref = [lambda x , y , z : psir.get_hf_orbs( frozen = frozen , virtual = virtual )] , active = active, frozen = frozen, virtual = virtual ,add_frozen = 0, add_virtual = 0)
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'] , [[1,2],[2]], [] , fname = detfile11 ,add_frozen = 0, add_virtual = 0,ref = [ lambda x , y , z : psir.get_hf_orbs()] ) #CISDD
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'] , [[1,2],[]], [0] , fname = detfile2 ,add_frozen = 0, add_virtual = 0,ref = [ lambda x , y , z : psir.get_hf_orbs()] ) #CISDDOCI
dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[[], [1]], [] , fname = detfile3 ,add_frozen = 0, ref = [lambda x , y , z : psir.get_hf_orbs()]) #CIS(P)
dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[[], [1,2]], [] , fname = detfile4 ,add_frozen = 0, ref = [lambda x , y , z : psir.get_hf_orbs()]) #CISD(P)
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[[1,2], [] ],[] , fname = detfile1 ,add_frozen = 0, ref = [lambda x , y , z : psir.get_hf_orbs()]) #CISD
#dw.cimain(psir.values['nalpha']-1,psir.values['nbeta']-1, psir.values['norb']-1,[[1,2,3,4], [] ],[] , fname = detfile6 ,add_frozen = 1, ref = [lambda x , y , z : dw.get_hf_det(x,y,z)] ) #FCI
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[range(1,psir.values['nbeta']*2 +1), [] ],[] , fname = detfile6 ,add_frozen = 0, ref = [lambda x , y , z : dw.get_hf_det(x,y,z)] ) #FCI
afh = 'R'
for basis in basissets:
fname = "ciflowresults_" + basis + ".dat"
with open(fname , 'w') as f:
header = ht.create_header(afh , methods,psienergies)
print header
f.write(header)
for index , matrixelements in enumerate(hamfiles.plotfiles):
psir = rp.PsiReader(matrixelements, isbig = False, numorbs = -1 , read_ints = False)
if active_space:
psir.set_active_space([0] , [[1,2],[]] , [] , detfile1) #for pisystem of deformed benzene
psir.set_active_space([0] , [[1,2], [2]] , [] , detfile11) #for pisystem of deformed benzene
ht.create_ciflow_input_file(matrixelements , methods , fname = flowname)
ci_flow =""
try:
process = subprocess.Popen(["./ciflow_%s.x" %pokemon ] , stdin =open(flowname , 'r'), stdout = subprocess.PIPE)
for line in iter(process.stdout.readline, ''):
sys.stdout.write(line)
ci_flow += line
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
"""
try:
ci_flow = subprocess.check_output(['./ciflow_%s.x' %pokemon ] , stdin =open(flowname , 'r') )
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
"""
energies = ht.process_output(ci_flow) + [x[1] for x in psir.extract_energies()]
ht.print_output(matrixelements, energies , methods)
f.write("%.15f\t%s\n" %(runlist[index], '\t'.join(energies )) )
os.remove('./ciflow_%s.x' %pokemon)
os.remove('./mointegrals.so')
#os.remove(detfile1)
ht.generate_dir('output_files', None, prefix = r'output[\w_]+.dat')
os.chdir('..')
ht.generate_dir('unitaries', None, prefix = 'unitary_')
os.chdir('..')
ht.generate_dir('matrixelements_otherbasis', None, prefix = 'hamp')
os.chdir('..')
OUTPUTDIR = os.path.join(ORIGDIR, name+str(arrayid) )
print 'We Start to create the outputdir ' , OUTPUTDIR
if os.path.isdir(OUTPUTDIR):
shutil.rmtree(OUTPUTDIR)
make_tarfile(OUTPUTDIR , WORKDIR)
DATADIR = os.path.join(os.getenv('VSC_DATA'), name + str(arrayid) + os.getenv('PBS_JOBID'))
make_tarfile(DATADIR, WORKDIR)
print 'We made a copy of the jobdata to: ', DATADIR
def hub1d():
pokemon = os.environ['VSC_INSTITUTE_CLUSTER']
flowname = "flow.dat"
psienergies = []
methods = ["fci" , "none"]
nalpha = 4
norb = 8
options = ['notzero' , 'pos', 'per']
name = 'hub1dmpdnorb' + str(norb) + 'pair' + str(nalpha) + options[2] + 'U0-100' #relative to the directory that contains this script
import numpy as np
runlist = range(0,101)
runlist = [0.1 , 1 , 4, 10 , 100]
modtype = 'Hub1d' ; params = [1. , 4.]
arrayid = 2
#hereunder for array jobs for heavy calculations. But make sure it is always defined
#arrayid =int(os.getenv('PBS_ARRAYID'))
#arraystep = 1
#name += str(arrayid)
#try:
# runlist = runlist[(arrayid-1) * arraystep : arrayid *arraystep]
#except:
# print 'encoutered exception in cut of runlist.'
# runlist = runlist[-4:-1]
print 'Start to load necessary modules.'
os.system('module load cluster/%s' %pokemon)
os.system('module load PSI/4.0b6-20160201-intel-2016a-mt-Python-2.7.11')
os.system('module load arpack-ng/3.3.0-intel-2016a')
os.system('module load OpenBabel/2.3.2-intel-2014b-Python-2.7.8')
os.system('module load matplotlib')
os.system('module load h5py')
#os.system('module load Boost/1.55.0-ictce-7.1.2-Python-2.7.8')
os.system('export MKL_NUM_THREADS=16')
#os.system('export KMP_STACKSIZE=32m')
ORIGDIR= os.getenv('HOME')
mofile = os.path.join(ORIGDIR, 'devel/CIFlow/lib/mointegrals_%s.so' %pokemon)
exefile = os.path.join(ORIGDIR, 'devel/CIFlow/bin/ciflow_%s.x' %pokemon )
#hamdir = os.path.join(ORIGDIR, hamdirname)
#det_file = os.path.join(ORIGDIR, detfile10 )
print 'We submitted the script in: ', ORIGDIR
print 'Psi 4 plugin is at: ' , mofile
WORKDIR= os.path.join(os.getenv('VSC_SCRATCH_NODE'),os.getenv('PBS_JOBID'))
if os.path.isdir(WORKDIR):
shutil.rmtree(WORKDIR)
os.mkdir(WORKDIR)
print 'Workdir is: ', WORKDIR
shutil.copy(mofile,WORKDIR)
shutil.copy(exefile,WORKDIR)
#hamdest = os.path.join(WORKDIR, hamdirname)
#shutil.copytree(hamdir,hamdest)
#shutil.move(det_file,WORKDIR)
os.chdir(WORKDIR)
print 'We work on node: ' , os.getenv('HOSTNAME')
create_modham_input(nalpha , norb , modtype , options , params , runlist)
fileinfo = lambda x: float(re.search(r'run[-\w\d=]*([\-+]?\d+[\.,]?\d*[eEDd]?[\-+]?\d*)\.mod' , x).group(1))
search = modtype+ '.+mod'
hamfiles= File_Collector('.', search = search ,notsearch = r'\.sw\w',sortfunction = fileinfo, filterf = lambda x : fileinfo(x) >= -1 and fileinfo(x) < 1000. )
print 'Contents of rundir before run are: ', os.listdir(os.getcwd())
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[[], [1]], [] , fname = detfile3 ,add_frozen = 0, ref = [lambda x , y , z : psir.get_hf_orbs()]) #CIS(P)
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'], psir.values['norb'],[[], [1,2]], [] , fname = detfile4 ,add_frozen = 0, ref = [lambda x , y , z : psir.get_hf_orbs()]) #CISD(P)
afh = 'R'
fname = "ciflowresults.dat"
with open(fname , 'w') as f:
header = ht.create_header(afh , methods,psienergies)
print header
f.write(header)
for index , matrixelements in enumerate(hamfiles.plotfiles):
ht.create_ciflow_input_file(matrixelements , methods , fname = flowname)
ci_flow =""
try:
process = subprocess.Popen(["./ciflow_%s.x" %pokemon ] , stdin =open(flowname , 'r'), stdout = subprocess.PIPE)
for line in iter(process.stdout.readline, ''):
sys.stdout.write(line)
ci_flow += line
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
"""
try:
ci_flow = subprocess.check_output(['./ciflow_%s.x' %pokemon ] , stdin =open(flowname , 'r') )
except Exception as e:
print 'Ciflow gave the following error', e
print ci_flow
pass
"""
energies = ht.process_output(ci_flow)
ht.print_output(matrixelements, energies , methods)
f.write("%.15f\t%s\n" %(runlist[index], '\t'.join(energies )) )
os.remove('./ciflow_%s.x' %pokemon)
os.remove('./mointegrals.so')
#os.remove(detfile1)
ht.generate_dir('output_files', None, prefix = r'output[\w_]+.dat')
os.chdir('..')
ht.generate_dir('unitaries', None, prefix = 'unitary_')
os.chdir('..')
ht.generate_dir('matrixelements_otherbasis', None, prefix = 'hamp')
os.chdir('..')
OUTPUTDIR = os.path.join(ORIGDIR, name+str(arrayid) )
print 'We Start to create the outputdir ' , OUTPUTDIR
if os.path.isdir(OUTPUTDIR):
shutil.rmtree(OUTPUTDIR)
make_tarfile(OUTPUTDIR , WORKDIR)
DATADIR = os.path.join(os.getenv('VSC_DATA'), name + str(arrayid) + os.getenv('PBS_JOBID'))
make_tarfile(DATADIR, WORKDIR)
print 'We made a copy of the jobdata to: ', DATADIR
