Exemple #1
0
#
# This script generates a simple H2 input and writes it to disk
#
# MBG (2/2014)
#
#

import pyqchem as qc

#make the rem array and define the basis and exchange (setting them to defaults, but showing how)
rem=qc.rem_array()
rem.basis("sto-3g")
rem.exchange("hf")

#make the cartesian object
xyz=qc.cartesian()
xyz.add_atom() #defaults to H at origin
xyz.add_atom("H","0","0",".74")

#make molecule array from cartesian object
molec=qc.mol_array(xyz)

#make input object and write to disk
job=qc.inputfile()
job.add(rem)
job.add(molec)
job.write("h2.in")
Exemple #2
0
rem1.scf_convergence("10")
from copy import deepcopy
rem2 = deepcopy(rem1)
rem2.scf_guess("fragmo")

#make a rem_frgm array
rem_frgm = qc.rem_frgm_array()
rem_frgm.thresh("7")
rem_frgm.scf_convergence("3")

#make objects for holding the molecular geometries
xyz = qc.read("4water.xyz")
frag = qc.fragment(atom_list=xyz.list_of_atoms)

#make molecule array from cartesian object
mol1 = qc.mol_array(xyz)
mol2 = qc.mol_array(frag)

#make input object and write to disk
job1 = qc.inputfile()
job1.add(rem1)
job1.add(mol1)

job2 = qc.inputfile()
job2.add(rem2)
job2.rem.scf_guess("fragmo")
job2.add(rem_frgm)
job2.add(mol2)

job = qc.multifile()
job.add(job1)
Exemple #3
0
import pyqchem as qc
import os

#make a generic rem array
rem=qc.rem_array()
rem.basis("sto-3g")
rem.exchange("hf")

#make a list of jobs
job_list=[]

#for all xyzs in a database, create and append the job to the list
for i in os.popen("ls ../../databases/a24/*.xyz").read().splitlines():

    #make the jobs
    job=qc.inputfile()

    #give job a name
    job.runinfo.name=i.split('/')[-1].replace(".xyz","")

    #read the xyz
    xyz=qc.read(i)
   
    #append the molecule and rem array
    job.add(qc.mol_array(xyz))
    job.add(rem)
    job_list.append(job)

# run all jobs in list using 12 workers
qc.queue(job_list,num_workers=12)
Exemple #4
0
rem1.scf_convergence("10")
from copy import deepcopy
rem2=deepcopy(rem1)
rem2.scf_guess("fragmo")

#make a rem_frgm array
rem_frgm=qc.rem_frgm_array()
rem_frgm.thresh("7")
rem_frgm.scf_convergence("3")

#make objects for holding the molecular geometries
xyz=qc.read("4water.xyz")
frag=qc.fragment(atom_list=xyz.list_of_atoms)

#make molecule array from cartesian object
mol1=qc.mol_array(xyz)
mol2=qc.mol_array(frag)

#make input object and write to disk
job1=qc.inputfile()
job1.add(rem1)
job1.add(mol1)

job2=qc.inputfile()
job2.add(rem2)
job2.rem.scf_guess("fragmo")
job2.add(rem_frgm)
job2.add(mol2)

job=qc.multifile()
job.add(job1)
Exemple #5
0
# MBG (2/2014)
#
import pyqchem as qc

#make the rem array and fill it
rem = qc.rem_array()
rem.basis("sto-3g")
rem.jobtype("opt")

#make the cartesian object and fill it
xyz = qc.cartesian()
xyz.add_atom()  #defaults to H at origin
xyz.add_atom("H", "0", "0", ".74")

#make molecule array from cartesian object
molec = qc.mol_array(xyz)

#assemble the job from the arrays
job1 = qc.inputfile()
job1.add(rem)
job1.add(molec)

#write it to file
job1.write("h2.in")

#make another rem to do the second job
rem2 = qc.deepcopy(rem)
rem2.jobtype("freq")

#define the  molecule array as "READ" so we grab the right geometry
molec2 = qc.mol_array()
Exemple #6
0
import pyqchem as qc
import os

#make a generic rem array
rem = qc.rem_array()
rem.basis("sto-3g")
rem.exchange("hf")

#make a list of jobs
job_list = []

#for all xyzs in a database, create and append the job to the list
for i in os.popen("ls ../../databases/a24/*.xyz").read().splitlines():

    #make the jobs
    job = qc.inputfile()

    #give job a name
    job.runinfo.name = i.split('/')[-1].replace(".xyz", "")

    #read the xyz
    xyz = qc.read(i)

    #append the molecule and rem array
    job.add(qc.mol_array(xyz))
    job.add(rem)
    job_list.append(job)

# run all jobs in list using 12 workers
qc.queue(job_list, num_workers=12)
Exemple #7
0
#
import pyqchem as qc


#make the rem array and fill it
rem=qc.rem_array()
rem.basis("sto-3g")
rem.jobtype("opt")

#make the cartesian object and fill it
xyz=qc.cartesian()
xyz.add_atom() #defaults to H at origin
xyz.add_atom("H","0","0",".74")

#make molecule array from cartesian object
molec=qc.mol_array(xyz)

#assemble the job from the arrays
job1=qc.inputfile()
job1.add(rem)
job1.add(molec)

#write it to file
job1.write("h2.in")

#make another rem to do the second job
rem2=qc.deepcopy(rem)
rem2.jobtype("freq")

#define the  molecule array as "READ" so we grab the right geometry
molec2=qc.mol_array()