Source code for molutil

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"""Module with utility functions that act on molecule objects."""
import os
import re
import subprocess
import socket
import shutil
import random
import math
import psi4
import p4const
import p4util
from p4regex import *
from dashparam import *


[docs]def extract_clusters(mol, ghost=True, cluster_size=0): """Function to return all subclusters of the molecule *mol* of real size *cluster_size* and all other atoms ghosted if *ghost* equals true, all other atoms discarded if *ghost* is false. If *cluster_size* = 0, returns all possible combinations of cluster size. """ # How many levels of clusters are possible? nfrag = mol.nfragments() # Initialize the cluster array clusters = [] # scope the arrays reals = [] ghosts = [] # counter counter = 0 # loop over all possible cluster sizes for nreal in range(nfrag, 0, -1): # if a specific cluster size size is requested, only do that if (nreal != cluster_size and cluster_size > 0): continue # initialize the reals list reals = [] # setup first combination [3,2,1] lexical ordering # fragments indexing is 1's based, bloody hell for index in range(nreal, 0, -1): reals.append(index) # start loop through lexical promotion while True: counter = counter + 1 # Generate cluster from last iteration if (ghost): ghosts = [] for g in range(nfrag, 0, -1): if (g not in reals): ghosts.append(g) #print "Cluster #%d: %s reals, %s ghosts" % (counter,str(reals), str(ghosts)) clusters.append(mol.extract_subsets(reals, ghosts)) else: #print "Cluster #%d: %s reals" % (counter,str(reals)) clusters.append(mol.extract_subsets(reals)) # reset rank rank = 0 # look for lexical promotion opportunity # i.e.: [4 2 1] has a promotion opportunity at # index 1 to produce [4 3 1] for k in range(nreal - 2, -1, -1): if (reals[k] != reals[k + 1] + 1): rank = k + 1 break # do the promotion reals[rank] = reals[rank] + 1 # demote the right portion of the register val = 1 for k in range(nreal - 1, rank, -1): reals[k] = val val = val + 1 # boundary condition is promotion into # [nfrag+1 nfrag-1 ...] if (reals[0] > nfrag): break return clusters
[docs]def extract_cluster_indexing(mol, cluster_size=0): """Function to returns a LIST of all subclusters of the molecule *mol* of real size *cluster_size*. If *cluster_size* = 0, returns all possible combinations of cluster size. """ import copy # How many levels of clusters are possible? nfrag = mol.nfragments() # Initialize the cluster array clusters = [] # scope the arrays reals = [] # counter counter = 0 # loop over all possible cluster sizes for nreal in range(nfrag, 0, -1): # if a specific cluster size size is requested, only do that if (nreal != cluster_size and cluster_size > 0): continue # initialize the reals list reals = [] # setup first combination [3,2,1] lexical ordering # fragments indexing is 1's based, bloody hell for index in range(nreal, 0, -1): reals.append(index) # start loop through lexical promotion while True: counter = counter + 1 # Generate cluster from last iteration clusters.append(copy.deepcopy(reals)) # reset rank rank = 0 # look for lexical promotion opportunity # i.e.: [4 2 1] has a promotion opportunity at # index 1 to produce [4 3 1] for k in range(nreal - 2, -1, -1): if (reals[k] != reals[k + 1] + 1): rank = k + 1 break # do the promotion reals[rank] = reals[rank] + 1 # demote the right portion of the register val = 1 for k in range(nreal - 1, rank, -1): reals[k] = val val = val + 1 # boundary condition is promotion into # [nfrag+1 nfrag-1 ...] if (reals[0] > nfrag): break return clusters
[docs]def new_set_attr(self, name, value): """Function to redefine __setattr__ method of molecule class.""" fxn = object.__getattribute__(self, "is_variable") isvar = fxn(name) if isvar: fxn = object.__getattribute__(self, "set_variable") fxn(name, value) return object.__setattr__(self, name, value)
[docs]def new_get_attr(self, name): """Function to redefine __getattr__ method of molecule class.""" fxn = object.__getattribute__(self, "is_variable") isvar = fxn(name) if isvar: fxn = object.__getattribute__(self, "get_variable") return fxn(name) return object.__getattribute__(self, name)
[docs]def BFS(self): """Perform a breadth-first search (BFS) on the real atoms in molecule, returning an array of atom indices of fragments. Relies upon van der Waals radii and so faulty for close (esp. hydrogen-bonded) fragments. Original code from Michael S. Marshall. """ vdW_diameter = { 'H': 1.001 / 1.5, 'HE': 1.012 / 1.5, 'LI': 0.825 / 1.5, 'BE': 1.408 / 1.5, 'B': 1.485 / 1.5, 'C': 1.452 / 1.5, 'N': 1.397 / 1.5, 'O': 1.342 / 1.5, 'F': 1.287 / 1.5, 'NE': 1.243 / 1.5, 'NA': 1.144 / 1.5, 'MG': 1.364 / 1.5, 'AL': 1.639 / 1.5, 'SI': 1.716 / 1.5, 'P': 1.705 / 1.5, 'S': 1.683 / 1.5, 'CL': 1.639 / 1.5, 'AR': 1.595 / 1.5} Queue = [] White = range(self.natom()) # untouched Black = [] # touched and all edges discovered Fragment = [] # stores fragments start = 0 # starts with the first atom in the list Queue.append(start) White.remove(start) # Simply start with the first atom, do a BFS when done, go to any # untouched atom and start again iterate until all atoms belong # to a fragment group while len(White) > 0 or len(Queue) > 0: # Iterates to the next fragment Fragment.append([]) while len(Queue) > 0: # BFS within a fragment for u in Queue: # find all (still white) nearest neighbors to vertex u for i in White: dist = p4const.psi_bohr2angstroms * math.sqrt((self.x(i) - self.x(u)) ** 2 + \ (self.y(i) - self.y(u)) ** 2 + (self.z(i) - self.z(u)) ** 2) if dist < vdW_diameter[self.symbol(u)] + vdW_diameter[self.symbol(i)]: Queue.append(i) # if you find you, put in the queue White.remove(i) # and remove it from the untouched list Queue.remove(u) # remove focus from Queue Black.append(u) Fragment[-1].append(int(u)) # add to group (0-indexed) Fragment[-1].sort() # preserve original atom ordering if len(White) != 0: # can't move White -> Queue if no more exist Queue.append(White[0]) White.remove(White[0]) return Fragment
[docs]def run_dftd3(self, func=None, dashlvl=None, dashparam=None, dertype=None): """Function to call Grimme's dftd3 program (http://toc.uni-muenster.de/DFTD3/) to compute the -D correction of level *dashlvl* using parameters for the functional *func*. The dictionary *dashparam* can be used to supply a full set of dispersion parameters in the absense of *func* or to supply individual overrides in the presence of *func*. Returns energy if *dertype* is 0, gradient if *dertype* is 1, else tuple of energy and gradient if *dertype* unspecified. The dftd3 executable must be independently compiled and found in :envvar:`PATH`. """ # Validate arguments if self is None: self = psi4.get_active_molecule() dashlvl = dashlvl.lower() dashlvl = dash_alias['-' + dashlvl][1:] if ('-' + dashlvl) in dash_alias.keys() else dashlvl if dashlvl not in dashcoeff.keys(): raise ValidationError("""-D correction level %s is not available. Choose among %s.""" % (dashlvl, dashcoeff.keys())) if dertype is None: dertype = -1 elif der0th.match(str(dertype)): dertype = 0 elif der1st.match(str(dertype)): dertype = 1 elif der2nd.match(str(dertype)): raise ValidationError('Requested derivative level \'dertype\' %s not valid for run_dftd3.' % (dertype)) else: raise ValidationError('Requested derivative level \'dertype\' %s not valid for run_dftd3.' % (dertype)) if func is None: if dashparam is None: # defunct case raise ValidationError("""Parameters for -D correction missing. Provide a func or a dashparam kwarg.""") else: # case where all param read from dashparam dict (which must have all correct keys) func = 'custom' dashcoeff[dashlvl][func] = {} dashparam = dict((k.lower(), v) for k, v in dashparam.iteritems()) for key in dashcoeff[dashlvl]['b3lyp'].keys(): if key in dashparam.keys(): dashcoeff[dashlvl][func][key] = dashparam[key] else: raise ValidationError("""Parameter %s is missing from dashparam dict %s.""" % (key, dashparam)) else: func = func.lower() if func not in dashcoeff[dashlvl].keys(): raise ValidationError("""Functional %s is not available for -D level %s.""" % (func, dashlvl)) if dashparam is None: # (normal) case where all param taken from dashcoeff above pass else: # case where items in dashparam dict can override param taken from dashcoeff above dashparam = dict((k.lower(), v) for k, v in dashparam.iteritems()) for key in dashcoeff[dashlvl]['b3lyp'].keys(): if key in dashparam.keys(): dashcoeff[dashlvl][func][key] = dashparam[key] # Move ~/.dftd3par.<hostname> out of the way so it won't interfere defaultfile = os.path.expanduser('~') + '/.dftd3par.' + socket.gethostname() defmoved = False if os.path.isfile(defaultfile): os.rename(defaultfile, defaultfile + '_hide') defmoved = True # Setup unique scratch directory and move in current_directory = os.getcwd() psioh = psi4.IOManager.shared_object() psio = psi4.IO.shared_object() os.chdir(psioh.get_default_path()) dftd3_tmpdir = 'psi.' + str(os.getpid()) + '.' + psio.get_default_namespace() + \ '.dftd3.' + str(random.randint(0, 99999)) if os.path.exists(dftd3_tmpdir) is False: os.mkdir(dftd3_tmpdir) os.chdir(dftd3_tmpdir) # Write dftd3_parameters file that governs dispersion calc paramfile = './dftd3_parameters' pfile = open(paramfile, 'w') pfile.write(dash_server(func, dashlvl, 'dftd3')) pfile.close() # Write dftd3_geometry file that supplies geometry to dispersion calc geomfile = './dftd3_geometry.xyz' gfile = open(geomfile, 'w') numAtoms = self.natom() geom = self.save_string_xyz() reals = [] for line in geom.splitlines(): if line.split()[0] == 'Gh': numAtoms -= 1 else: reals.append(line) gfile.write(str(numAtoms)+'\n') for line in reals: gfile.write(line.strip()+'\n') gfile.close() # Call dftd3 program try: dashout = subprocess.Popen(['dftd3', geomfile, '-grad'], stdout=subprocess.PIPE) except OSError: raise ValidationError('Program dftd3 not found in path.') out, err = dashout.communicate() # Parse output (could go further and break into E6, E8, E10 and Cn coeff) success = False for line in out.splitlines(): if re.match(' Edisp /kcal,au', line): sline = line.split() dashd = float(sline[3]) if re.match(' normal termination of dftd3', line): success = True if not success: raise ValidationError('Program dftd3 did not complete successfully.') # Parse grad output derivfile = './dftd3_gradient' dfile = open(derivfile, 'r') dashdderiv = [] i = 0 for line in geom.splitlines(): if i == 0: i += 1 else: if line.split()[0] == 'Gh': dashdderiv.append([0.0, 0.0, 0.0]) else: temp = dfile.readline() dashdderiv.append([float(x.replace('D', 'E')) for x in temp.split()]) dfile.close() if len(dashdderiv) != self.natom(): raise ValidationError('Program dftd3 gradient file has %d atoms- %d expected.' % \ (len(dashdderiv), self.natom())) psi_dashdderiv = psi4.Matrix(self.natom(), 3) psi_dashdderiv.set(dashdderiv) # Print program output to file if verbose verbose = psi4.get_option('SCF', 'PRINT') if verbose >= 3: psi4.print_out('\n ==> DFTD3 Output <==\n') psi4.print_out(out) dfile = open(derivfile, 'r') psi4.print_out(dfile.read().replace('D', 'E')) dfile.close() psi4.print_out('\n') # Clean up files and remove scratch directory os.unlink(paramfile) os.unlink(geomfile) os.unlink(derivfile) if defmoved is True: os.rename(defaultfile + '_hide', defaultfile) os.chdir('..') try: shutil.rmtree(dftd3_tmpdir) except OSError as e: ValidationError('Unable to remove dftd3 temporary directory %s' % e, file=sys.stderr) os.chdir(current_directory) # return -D & d(-D)/dx psi4.set_variable('DISPERSION CORRECTION ENERGY', dashd) if dertype == -1: return dashd, dashdderiv elif dertype == 0: return dashd elif dertype == 1: return psi_dashdderiv
[docs]def dynamic_variable_bind(cls): """Function to dynamically add extra members to the psi4.Molecule class. """ cls.__setattr__ = new_set_attr cls.__getattr__ = new_get_attr cls.BFS = BFS cls.run_dftd3 = run_dftd3
dynamic_variable_bind(psi4.Molecule) # pass class type, not class instance # # Define geometry to be used by PSI4. # The molecule created by this will be set in options. # # geometry(" # O 1.0 0.0 0.0 # H 0.0 1.0 0.0 # H 0.0 0.0 0.0 #
[docs]def geometry(geom, name="default"): """Function to create a molecule object of name *name* from the geometry in string *geom*. """ molecule = psi4.Molecule.create_molecule_from_string(geom) molecule.set_name(name) activate(molecule) return molecule
[docs]def activate(mol): """Function to set molecule object *mol* as the current active molecule.""" psi4.set_active_molecule(mol) #psi4.IO.set_default_namespace(mol.get_name())