def set_active_space(self, irreplist , exlist , senlist, detfile ):
"""
Generates a determinantfile in a given active space determined by irreps. Remark at this moment the active space should be concatenated without gaps.
"""
self.set_irrep_info() #to set the cumulative array of orbital indices where new irreps start.
nup, ndown, norb = 0, 0 ,0
activehf = [[],[]]
for irrep in irreplist:
nup += self.values['DOCC'][irrep]
ndown += self.values['DOCC'][irrep]
nup += self.values['SOCC'][irrep]
norb += self.occurences[irrep]
activehf[0] += [1]*self.values['DOCC'][irrep] + [0] * (self.occurences[irrep] - self.values['DOCC'][irrep])
activehf[1] += [1]*self.values['DOCC'][irrep] + [0] * (self.occurences[irrep] - self.values['DOCC'][irrep])
activehf[0].reverse()
activehf[1].reverse()
activehf = ( ''.join(map(str,activehf[0])) , ''.join(map(str, activehf[1]) ) )
upstring , downstring = self.get_hf_orbs() #to determine the frozen orbitals
frozen = upstring[-self.cum[irreplist[0]] :] #we presume that if there is an odd number of electrons, it is in the activespace.
virtual = upstring[:-1*(self.cum[irreplist[-1] + 1 ] ) ]
print 'frozen' , frozen , 'virtual' , virtual
dw.cimain(nup,ndown ,norb , [range(1,nup+ndown+1), [] ] , senlist ,fname = detfile ,ref = [lambda x , y, z : activehf ], add_frozen = 0, frozenstring = frozen , virtualstring = virtual)
def main_opt(*args, **kwargs):
ciflowoutputfile = "ciflowoutput2.txt"
flowname = "flow.dat"
detfile1 = "determinants1.dat"
detfile2 = "determinants2.dat"
detfile3 = "determinants3.dat"
detfile4 = "determinants4.dat"
detfile5 = "determinants5.dat"
detfile6 = "determinants6.dat"
detfile7 = "frozencisdpibenzene.dat"
detfile8 = "cisdpibenzenesigma.dat"
detfile9 = "CISDirrepref+cisd.dat"
detfile10 = "CISDT(P).dat"
detfile11 = "lin_hyb.dat"
detfile12 = "ref2.dat"
detfile20 = "sen0.dat"
detfile21 = "sen2.dat"
detfile22 = "sen4.dat"
detfile23 = "sen6.dat"
detfile24 = "sen8.dat"
detfile25 = "sen10.dat"
detfile30 = "sen0-4.dat"
change_ints = False # if you changed the standard psi4 integrals somewhere during the process
psienergies = [] # provide here a list of energies to be calculated by psi.
methods = ["file", detfile2, "mmind", "file", detfile3] + ["doci", "local", "file", detfile21, "file", detfile22]
methods = ["file", detfile30]
extra = None
basissets = ["6-31g"]
import numpy as np
runlist = np.arange(5.1, 8.1, 0.01)
# atoms = [6 , 8]
# atoms = [4]
# atoms = [1,1,1,1 , 1, 1]
atoms = [4, 1, 1]
# atoms = [4,1,1] #beh2
# atoms = [7,7]
# atoms = [7,8] #NO+
# atoms = [6,6,6,6,6,6,1,1,1,1,1,1] #benzene
# runlist = [x*math.pi/180. for x in range(55,61) ]#+ [59.5]] #, 60] ] #angle between two triangles in benzene.
name = "phdsenhierbeh2sen04cisdmmin"
rootdir = "./results/phdsenhierbeh26-31g2" # relative to the directory that contains this script
# rootdir = './results/phdsenebeccpvdzfcimminc1' #relative to the directory that contains this script
exe = "ciflow.x"
elemdir = "matrixelements"
# elemdir = 'matrixelements_otherbasis'
# elemdir = 'random_hamiltonians'
# elemdir = 'output_run'
elemdir = "."
# generate_dir(rootdir , exe )
# generate_dir(rootdir , exe , args= ["ni_system.dat"], prefix = r'./ham_patrick/hamnoplus')
# generate_dir(rootdir , exe )
# generate_dir(rootdir , exe , args= ["ni_system.dat"])
shutil.copy(exe, rootdir) # When the matrixelements are already present.
os.chdir(rootdir) # When the matrixelements are already present.
# create_matrix_elements(elemdir , basissets, runlist, atoms, chmult = (0,1) , moltype = 'h6', package = 'psi' , units = 'angstrom', path_mo = '../../../../mointegrals/mointegrals.so' , DOCC = None, energies = psienergies, sym = 'c1', hdf5 = False, guess = 'read', extrapar = 0.741, ref = 'rhf', su = False, basispath = '../../../data/basissets/')#, extrapar = 1.398) #extrapar is size for benzene, and angle for c2v, benzene extrapar = 1.398 C-C distance , extrapar = 104.479848 for angle h2o, 0.741 = extrapar for h2 equilibrium geometry in but
# create_matrix_elements(elemdir , basissets, runlist, atoms, chmult = (0,1) , moltype = 'atom', package = 'psi' , units = 'angstrom', path_mo = '../../../../mointegrals/mointegrals.so' , DOCC = None, energies = psienergies, sym = 'c1', hdf5 = False, guess = 'read', extrapar = 0.741, ref = 'rhf', su = False, basispath = '../../../data/basissets/')#, extrapar = 1.398) #extrapar is size for benzene, and angle for c2v, benzene extrapar = 1.398 C-C distance , extrapar = 104.479848 for angle h2o, 0.741 = extrapar for h2 equilibrium geometry in but
outputfile = open(ciflowoutputfile, "w")
# fileinfo = lambda x: float(re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*)[-\w\d]*\.[m]?out' , x).group(1))
fileinfo = lambda x: float(re.search(r"([\-+]?\d+[\.,]+\d+[eEd]?[\-+]?\d*)[-\w\d_]*\.[m]?dat", x).group(1))
# fileinfo = lambda x: float(re.search(r'FCIunit(\d+)\.[m]?dat' , x).group(1))
# fileinfo = lambda x: float(re.search(r'.*-[\w\d]*([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*)orthon\.h5' , x).group(1))
# fileinfo = lambda x: float(re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*)[-\w\d]*\.out' , x).group(1))
# fileinfo = lambda x: float(re.search(r'hamnoplussto-3gpatrick([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*)new\.out' , x).group(1))
hamfiles = {}
# search = r'psi.+%s.+mout'
search = r"hampsi0_%s.+2hmmin0.dat"
# search = r'hampsi0_%s.+local2.dat'
# search = 'hamnoplus.*%s.+out'
# search = r'hampsi.+%s.+FCI.+hmmin0.dat'
# search = r'randomham.+\d+\.dat'
# search = r'ham.+%s.+out'
# search = r'hampsi0.+%s.+smmind0.dat'
# search = r'ham.+%s.+FCIunit\d+\.dat'
# search = r'psi.+%s.+orthon.h5'
for basis in basissets:
hamfiles[basis] = fc.File_Collector(
elemdir,
search=search % basis,
notsearch=r"(\.sw\w)|(unitary)",
sortfunction=fileinfo,
filterf=lambda x: fileinfo(x) >= 5.1 and fileinfo(x) <= 1000.0,
)
# hamfiles[basis] = fc.File_Collector( '.', search = search %basis ,notsearch = r'\.sw\w',sortfunction = fileinfo, filterf = lambda x : fileinfo(x) <= 10. and fileinfo(x) >= 2 and fileinfo(x) in runlist and not '.sw' in x )
# hamfiles[basis] = fc.File_Collector(elemdir , search = search ,notsearch = r'\.sw\w',sortfunction = fileinfo, filterf = lambda x : fileinfo(x) >= -1 and fileinfo(x) < 1000. )
# fileinfo2 = lambda x: float(re.search(r'psi0_sto-3g1.29outputfciunit(\d+).dat' , x).group(1))
# search = r'psi.+outputfciunit\d+.dat'
# outputfilesfci = fc.File_Collector('output_files', search = search ,notsearch = r'\.sw\w',sortfunction = fileinfo2, filterf = lambda x : fileinfo2(x) >= 0 and fileinfo2(x) < 10000. )
# hamfiles[basissets[0]].plotfiles += ['ni_system.dat']
# print hamfiles[basissets[0]]
afh = "R"
for basis in basissets:
fname = name + "_" + basis + ".dat"
psir = rp.PsiReader(
hamfiles[basis].plotfiles[0], isbig=False, numorbs=-1, read_ints=False
) # just to get number of electrons and orbitals
# dw.generate_all_ex(psir.values['nalpha'],psir.values['nbeta'],psir.values['norb'], ( psir.get_hf_orbs()[0][:], psir.get_hf_orbs()[1][:] ) , aname = 'determinants', addfrozen = 0)
# dw.biggest_det_ex(outputfilesfci.plotfiles[index])
# dw.generate_all_sen(psir.values['nalpha'],psir.values['nbeta'],psir.values['norb'], 'sen', addfrozen = 0)
# reflist = dw.cimain(psir.values['nalpha'],psir.values['nbeta'] ,psir.values['norb'], [1] , [] , pairex = True)
dw.cimain(
psir.values["nalpha"] - 1,
psir.values["nbeta"] - 1,
psir.values["norb"] - 1,
[[], []],
[0, 4],
fname=detfile30,
ref=[lambda x, y, z: psir.get_hf_orbs()],
add_frozen=1,
) # CISD
# dw.cimain(psir.values['nalpha'],psir.values['nbeta'] ,psir.values['norb'],[[1,2,3] , []], [] ,fname = detfile14 ,ref = [lambda x , y , z : psir.get_hf_orbs()] ) #CISD
# dw.cimain(psir.values['nalpha'],psir.values['nbeta'] ,psir.values['norb'],[[1,2,3,4] , []], [] ,fname = detfile15 ,ref = [lambda x , y , z : psir.get_hf_orbs()] ) #CISD
# dw.cimain(psir.values['nalpha'],psir.values['nbeta'] ,psir.values['norb'],[[] ,[]], [0,2] ,fname = detfile2 ,ref = [lambda x , y , z : dw.get_hf_det(x,y,z)]) #SEN0-2
with open(fname, "w") as f:
header = create_header(afh, methods, psienergies, extra=extra)
print header
f.write(header)
for index, matrixelements in enumerate(hamfiles[basis].plotfiles):
print matrixelements
if change_ints: # True if you want to change the standard psi4 integrals.
psir = rp.PsiReader(matrixelements, isbig=True, numorbs=60, read_ints=True) # for benzene.
if "1.05" not in matrixelements:
# psir.set_active_space([1,2] , [1,2] , [] , detfile7) #for pisystem of deformed benzene
psir.set_active_space([1], [[1, 2], []], [], detfile7) # for pisystem of deformed benzene
else:
# psir.set_active_space([2,3,4,5] , [1,2] , [] , detfile7) #for pisystem of benzene
psir.set_active_space([1], [[1, 2], [2]], [], detfile7) # for pisystem of benzene
# psir.set_active_space([0,1,2,3] , [1] , [] , detfile3) #for pisystem of deformed benzene
# psir.set_active_space([1,2] , [1,2] , [] , detfile4) #for pisystem of deformed benzene
# psir.keep_orbs(56)
newname = os.path.basename(matrixelements) + "new.dat"
psir.create_output(newname)
matrixelements = newname
create_ciflow_input_file(matrixelements, methods, fname=flowname)
ci_flow = ""
if methods:
try:
ci_flow = ""
process = subprocess.Popen(["./ciflow.x"], 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
energies = process_output(ci_flow)
mullikencharge = process_output(
ci_flow, regexp="Mulliken[\s\w]+:\s*([\-+]?\d+[\.,]?\d*[eEDd]?[\-+]?\d*)"
)
if psienergies: # True if the list is not empty
psir = rp.PsiReader(matrixelements, isbig=False, numorbs=-1, read_ints=False)
energies += [x[1] for x in psir.extract_energies()]
print_output(matrixelements, energies, methods)
f.write("%.15f\t%s\t%s\n" % (runlist[index], "\t".join(energies), "\t".join(mullikencharge)))
if change_ints:
os.remove(matrixelements)
shutil.copy("../../htest.py", ".")
os.remove(exe) # can be handy to keep it in the dir, to exactly reproduce results later. (but be warned its big.)
outputfile.close()
try:
generate_dir("output_files", None, prefix=r"output[\w_]+.dat")
os.chdir("..")
generate_dir("unitaries", None, prefix="unitary_")
os.chdir("..")
generate_dir("matrixelements_otherbasis", None, prefix="hamp")
os.chdir("..")
except:
pass
if os.getenv("VSC_INSTITUTE_LOCAL") != "gent":
plotter = pf.Plot_Files(fname)
plotter.data[0].depvar["yas"] = "Energy" # change the future y-axis label
plotter.data[0].depvar["xas"] = "$R$" # is normally set to the column header 0
plotter.data[0].units["x"] = r"(\AA)"
plotter.data[0].units["y"] = r"(E$_h$)"
plotter.generate_plot(
xlimg=None, ylimg=None, exname="", prefix=True, titel=name, name=fname, depcol=0, ylist=None
)
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_opt(*args, **kwargs):
ciflowoutputfile = "ciflowoutput2.txt"
flowname = "flow.dat"
detfile1 = "determinants1.dat"
detfile2 = "determinants2.dat"
detfile3 = "determinants3.dat"
detfile4 = "determinants4.dat"
detfile5 = "determinants5.dat"
detfile6 = "determinants6.dat"
detfile7 = 'frozencisdpibenzene.dat'
detfile8 = 'cisdpibenzenesigma.dat'
detfile9 = 'CISDirrepref+cisd.dat'
detfile10 = "CISDT(P).dat"
detfile11 = "lin_hyb.dat"
detfile12 = "ref2.dat"
detfile20 = 'sen0.dat'
detfile21 = 'sen2.dat'
detfile22 = 'sen4.dat'
detfile23 = 'sen6.dat'
detfile24 = 'sen8.dat'
detfile25 = 'sen10.dat'
detfile30 = 'sen0-4.dat'
change_ints = False #if you changed the standard psi4 integrals somewhere during the process
psienergies = [] #provide here a list of energies to be calculated by psi.
methods = ["file", detfile2, "mmind", "file", detfile3
] + ["doci", "local", "file", detfile21, "file", detfile22]
methods = ["file", detfile30]
extra = None
basissets = ['6-31g']
import numpy as np
runlist = np.arange(5.1, 8.1, 0.01)
#atoms = [6 , 8]
#atoms = [4]
#atoms = [1,1,1,1 , 1, 1]
atoms = [4, 1, 1]
#atoms = [4,1,1] #beh2
#atoms = [7,7]
#atoms = [7,8] #NO+
#atoms = [6,6,6,6,6,6,1,1,1,1,1,1] #benzene
#runlist = [x*math.pi/180. for x in range(55,61) ]#+ [59.5]] #, 60] ] #angle between two triangles in benzene.
name = 'phdsenhierbeh2sen04cisdmmin'
rootdir = './results/phdsenhierbeh26-31g2' #relative to the directory that contains this script
#rootdir = './results/phdsenebeccpvdzfcimminc1' #relative to the directory that contains this script
exe = 'ciflow.x'
elemdir = 'matrixelements'
#elemdir = 'matrixelements_otherbasis'
#elemdir = 'random_hamiltonians'
#elemdir = 'output_run'
elemdir = '.'
#generate_dir(rootdir , exe )
#generate_dir(rootdir , exe , args= ["ni_system.dat"], prefix = r'./ham_patrick/hamnoplus')
#generate_dir(rootdir , exe )
#generate_dir(rootdir , exe , args= ["ni_system.dat"])
shutil.copy(exe, rootdir) #When the matrixelements are already present.
os.chdir(rootdir) #When the matrixelements are already present.
#create_matrix_elements(elemdir , basissets, runlist, atoms, chmult = (0,1) , moltype = 'h6', package = 'psi' , units = 'angstrom', path_mo = '../../../../mointegrals/mointegrals.so' , DOCC = None, energies = psienergies, sym = 'c1', hdf5 = False, guess = 'read', extrapar = 0.741, ref = 'rhf', su = False, basispath = '../../../data/basissets/')#, extrapar = 1.398) #extrapar is size for benzene, and angle for c2v, benzene extrapar = 1.398 C-C distance , extrapar = 104.479848 for angle h2o, 0.741 = extrapar for h2 equilibrium geometry in but
#create_matrix_elements(elemdir , basissets, runlist, atoms, chmult = (0,1) , moltype = 'atom', package = 'psi' , units = 'angstrom', path_mo = '../../../../mointegrals/mointegrals.so' , DOCC = None, energies = psienergies, sym = 'c1', hdf5 = False, guess = 'read', extrapar = 0.741, ref = 'rhf', su = False, basispath = '../../../data/basissets/')#, extrapar = 1.398) #extrapar is size for benzene, and angle for c2v, benzene extrapar = 1.398 C-C distance , extrapar = 104.479848 for angle h2o, 0.741 = extrapar for h2 equilibrium geometry in but
outputfile = open(ciflowoutputfile, 'w')
#fileinfo = lambda x: float(re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*)[-\w\d]*\.[m]?out' , x).group(1))
fileinfo = lambda x: float(
re.search(r'([\-+]?\d+[\.,]+\d+[eEd]?[\-+]?\d*)[-\w\d_]*\.[m]?dat', x).
group(1))
#fileinfo = lambda x: float(re.search(r'FCIunit(\d+)\.[m]?dat' , x).group(1))
#fileinfo = lambda x: float(re.search(r'.*-[\w\d]*([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*)orthon\.h5' , x).group(1))
#fileinfo = lambda x: float(re.search(r'([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*)[-\w\d]*\.out' , x).group(1))
#fileinfo = lambda x: float(re.search(r'hamnoplussto-3gpatrick([\-+]?\d+[\.,]?\d+[eEDd]?[\-+]?\d*)new\.out' , x).group(1))
hamfiles = {}
#search = r'psi.+%s.+mout'
search = r'hampsi0_%s.+2hmmin0.dat'
#search = r'hampsi0_%s.+local2.dat'
#search = 'hamnoplus.*%s.+out'
#search = r'hampsi.+%s.+FCI.+hmmin0.dat'
#search = r'randomham.+\d+\.dat'
#search = r'ham.+%s.+out'
#search = r'hampsi0.+%s.+smmind0.dat'
#search = r'ham.+%s.+FCIunit\d+\.dat'
#search = r'psi.+%s.+orthon.h5'
for basis in basissets:
hamfiles[basis] = fc.File_Collector(
elemdir,
search=search % basis,
notsearch=r'(\.sw\w)|(unitary)',
sortfunction=fileinfo,
filterf=lambda x: fileinfo(x) >= 5.1 and fileinfo(x) <= 1000.)
#hamfiles[basis] = fc.File_Collector( '.', search = search %basis ,notsearch = r'\.sw\w',sortfunction = fileinfo, filterf = lambda x : fileinfo(x) <= 10. and fileinfo(x) >= 2 and fileinfo(x) in runlist and not '.sw' in x )
#hamfiles[basis] = fc.File_Collector(elemdir , search = search ,notsearch = r'\.sw\w',sortfunction = fileinfo, filterf = lambda x : fileinfo(x) >= -1 and fileinfo(x) < 1000. )
#fileinfo2 = lambda x: float(re.search(r'psi0_sto-3g1.29outputfciunit(\d+).dat' , x).group(1))
#search = r'psi.+outputfciunit\d+.dat'
#outputfilesfci = fc.File_Collector('output_files', search = search ,notsearch = r'\.sw\w',sortfunction = fileinfo2, filterf = lambda x : fileinfo2(x) >= 0 and fileinfo2(x) < 10000. )
#hamfiles[basissets[0]].plotfiles += ['ni_system.dat']
#print hamfiles[basissets[0]]
afh = 'R'
for basis in basissets:
fname = name + "_" + basis + ".dat"
psir = rp.PsiReader(
hamfiles[basis].plotfiles[0],
isbig=False,
numorbs=-1,
read_ints=False) #just to get number of electrons and orbitals
#dw.generate_all_ex(psir.values['nalpha'],psir.values['nbeta'],psir.values['norb'], ( psir.get_hf_orbs()[0][:], psir.get_hf_orbs()[1][:] ) , aname = 'determinants', addfrozen = 0)
#dw.biggest_det_ex(outputfilesfci.plotfiles[index])
#dw.generate_all_sen(psir.values['nalpha'],psir.values['nbeta'],psir.values['norb'], 'sen', addfrozen = 0)
#reflist = dw.cimain(psir.values['nalpha'],psir.values['nbeta'] ,psir.values['norb'], [1] , [] , pairex = True)
dw.cimain(psir.values['nalpha'] - 1,
psir.values['nbeta'] - 1,
psir.values['norb'] - 1, [[], []], [0, 4],
fname=detfile30,
ref=[lambda x, y, z: psir.get_hf_orbs()],
add_frozen=1) #CISD
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'] ,psir.values['norb'],[[1,2,3] , []], [] ,fname = detfile14 ,ref = [lambda x , y , z : psir.get_hf_orbs()] ) #CISD
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'] ,psir.values['norb'],[[1,2,3,4] , []], [] ,fname = detfile15 ,ref = [lambda x , y , z : psir.get_hf_orbs()] ) #CISD
#dw.cimain(psir.values['nalpha'],psir.values['nbeta'] ,psir.values['norb'],[[] ,[]], [0,2] ,fname = detfile2 ,ref = [lambda x , y , z : dw.get_hf_det(x,y,z)]) #SEN0-2
with open(fname, 'w') as f:
header = create_header(afh, methods, psienergies, extra=extra)
print header
f.write(header)
for index, matrixelements in enumerate(hamfiles[basis].plotfiles):
print matrixelements
if change_ints: #True if you want to change the standard psi4 integrals.
psir = rp.PsiReader(matrixelements,
isbig=True,
numorbs=60,
read_ints=True) #for benzene.
if '1.05' not in matrixelements:
#psir.set_active_space([1,2] , [1,2] , [] , detfile7) #for pisystem of deformed benzene
psir.set_active_space(
[1], [[1, 2], []], [],
detfile7) #for pisystem of deformed benzene
else:
#psir.set_active_space([2,3,4,5] , [1,2] , [] , detfile7) #for pisystem of benzene
psir.set_active_space(
[1], [[1, 2], [2]], [],
detfile7) #for pisystem of benzene
#psir.set_active_space([0,1,2,3] , [1] , [] , detfile3) #for pisystem of deformed benzene
#psir.set_active_space([1,2] , [1,2] , [] , detfile4) #for pisystem of deformed benzene
#psir.keep_orbs(56)
newname = os.path.basename(matrixelements) + 'new.dat'
psir.create_output(newname)
matrixelements = newname
create_ciflow_input_file(matrixelements,
methods,
fname=flowname)
ci_flow = ""
if methods:
try:
ci_flow = ""
process = subprocess.Popen(["./ciflow.x"],
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
energies = process_output(ci_flow)
mullikencharge = process_output(
ci_flow,
regexp=
"Mulliken[\s\w]+:\s*([\-+]?\d+[\.,]?\d*[eEDd]?[\-+]?\d*)")
if psienergies: #True if the list is not empty
psir = rp.PsiReader(matrixelements,
isbig=False,
numorbs=-1,
read_ints=False)
energies += [x[1] for x in psir.extract_energies()]
print_output(matrixelements, energies, methods)
f.write("%.15f\t%s\t%s\n" %
(runlist[index], '\t'.join(energies),
'\t'.join(mullikencharge)))
if change_ints:
os.remove(matrixelements)
shutil.copy('../../htest.py', '.')
os.remove(
exe
) #can be handy to keep it in the dir, to exactly reproduce results later. (but be warned its big.)
outputfile.close()
try:
generate_dir('output_files', None, prefix=r'output[\w_]+.dat')
os.chdir('..')
generate_dir('unitaries', None, prefix='unitary_')
os.chdir('..')
generate_dir('matrixelements_otherbasis', None, prefix='hamp')
os.chdir('..')
except:
pass
if (os.getenv('VSC_INSTITUTE_LOCAL') != 'gent'):
plotter = pf.Plot_Files(fname)
plotter.data[0].depvar[
'yas'] = 'Energy' #change the future y-axis label
plotter.data[0].depvar[
'xas'] = '$R$' #is normally set to the column header 0
plotter.data[0].units['x'] = r'(\AA)'
plotter.data[0].units['y'] = r'(E$_h$)'
plotter.generate_plot(xlimg=None,
ylimg=None,
exname='',
prefix=True,
titel=name,
name=fname,
depcol=0,
ylist=None)
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
