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Merge pull request #68 from TimotheMelin/add_pyscf_implicit_solvent
Use PYSCF for PCM calculations
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| # Import both PySCF setup class | ||
| from pyscf_setup import PySCF_init_setup | ||
| from pyscf_setup import PySCF_post_run | ||
| import os | ||
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| def setup_frag_opt(poltype,newtorset,toranglelist,\ | ||
| pre,inputmol,inputname,inputstruc): | ||
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| """ | ||
| This function setup the PySCF file to do | ||
| a geometry optimization. | ||
| Inputs: | ||
| - poltype: poltype class object (class obj) | ||
| - newtorset: list of torsion to restrain (list of list) | ||
| - toranglelist: list of torsion angle to restrain (list of float) | ||
| - pre: prefix name (string) | ||
| - inputmol: molecule object (babel or rdkit mol obj) | ||
| - inputname: name of the input file (string) | ||
| - inputstruc: name if the file with input geometry (string) | ||
| Outputs: | ||
| - Opt_prep.PySCF_inp_file: Name of PySCF input file | ||
| - Opt_prep.PySCF_out_file: Name of PySCF output file | ||
| - cmd: command to run | ||
| """ | ||
|
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| # Define the charge of the molecule | ||
| charge = inputmol.GetTotalCharge() | ||
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| # Instantiate the PySCF initial setup object | ||
| Opt_prep = PySCF_init_setup(poltype,os.getcwd(),pre,inputmol,\ | ||
| False,charge) | ||
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| # Define the input geometry file | ||
| Opt_prep.PySCF_inp_xyz = inputstruc | ||
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| # Write the geometric constrain file | ||
| Opt_prep.write_geometric_tor_const(pre,newtorset) | ||
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| # Write the PySCF input file: is_opt = True, is_frag = True | ||
| Opt_prep.write_PySCF_input(True,True) | ||
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| # Define the command to run | ||
| cmd = f'python {Opt_prep.init_data["topdir"]}/{Opt_prep.PySCF_inp_file} &> {Opt_prep.init_data["topdir"]}/{Opt_prep.PySCF_out_file}' | ||
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| return Opt_prep.PySCF_inp_file,Opt_prep.PySCF_out_file,cmd | ||
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| def read_frag_opt(poltype,outputlog,mol): | ||
|
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| """ | ||
| This function creates the post run PySCf object and | ||
| reads the optimized geometry | ||
| Inputs: | ||
| - poltype: poltype class object (class obj) | ||
| - outputlog: Name of the output file (string) | ||
| - mol: molecule object (babel or rdkit mol obj) | ||
| """ | ||
|
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| # Instantiate the PySCF post run class | ||
| Opt_post = PySCF_post_run(poltype,os.getcwd(),outputlog,mol) | ||
|
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| # Read and create the optimized geometry file | ||
| Opt_post.read_out() | ||
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| def setup_frag_sp(poltype,inputmol,inputstruc,pre): | ||
|
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| """ | ||
| This function set up the fragment SP calculation | ||
| Inputs: | ||
| - poltype: poltype class object (class obj) | ||
| - inputmol: molecule object (babel or rdkit mol obj) | ||
| - inputstruc: name if the file with input geometry (string) | ||
| - pre: prefix name (string) | ||
| Outputs: | ||
| - Opt_prep.PySCF_inp_file: Name of PySCF input file | ||
| - Opt_prep.PySCF_out_file: Name of PySCF output file | ||
| - cmd: command to run | ||
| """ | ||
|
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||
| # Define the charge of the molecule | ||
| charge = inputmol.GetTotalCharge() | ||
|
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||
| # Instantiate the PySCF initial setup object | ||
| Opt_prep = PySCF_init_setup(poltype,os.getcwd(),pre,inputmol,\ | ||
| False,charge) | ||
|
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| # Define the input geometry file | ||
| Opt_prep.PySCF_inp_xyz = inputstruc | ||
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| # Write the PySCF input file: is_opt = False, is_frag = True | ||
| Opt_prep.write_PySCF_input(False,True) | ||
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| # Define the command to run | ||
| cmd = f'python {Opt_prep.init_data["topdir"]}/{Opt_prep.PySCF_inp_file} &> {Opt_prep.init_data["topdir"]}/{Opt_prep.PySCF_out_file}' | ||
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| return Opt_prep.PySCF_inp_file,Opt_prep.PySCF_out_file,cmd | ||
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