Exemplo n.º 1
0
 def read_quantum():
     Result = None
     os.chdir('calcs')
     for i in range(M.ns):
         dnm = eval(formstr % i)
         print("\rNow in directory %i" % i, end=' ')
         if os.path.exists(dnm):
             os.chdir(dnm)
             if os.path.exists('qchem.out'):
                 Output = Molecule('qchem.out')
                 if os.path.exists('plot.esp'):
                     ESP = Molecule('plot.esp')
                     #print ESP.Data.keys()
                     Output.qm_espxyzs = list(ESP.qm_espxyzs)
                     Output.qm_espvals = list(ESP.qm_espvals)
                     #Output += Molecule('plot.esp')
                 if Result == None:
                     Result = Output
                 else:
                     Result += Output
             else:
                 raise Exception("The output file %s doesn't exist." % os.path.abspath('qchem.out'))
             os.chdir('..')
         else:
             raise Exception("The subdirectory %s doesn't exist." % os.path.abspath(dnm))
     os.chdir('..')
     return Result
Exemplo n.º 2
0
def gather_generations():
    shots = Molecule('shots.gro')
    qdata = Molecule('qdata.txt')
    A1    = np.array(shots.xyzs)
    A2    = np.array(qdata.xyzs)
    if A1.shape != A2.shape:
        raise Exception('shots.gro and qdata.txt appear to contain different data')
    elif np.max(np.abs((A1 - A2).flatten())) > 1e-4:
        raise Exception('shots.gro and qdata.txt appear to contain different xyz coordinates')
    shots.qm_energies = qdata.qm_energies
    shots.qm_forces   = qdata.qm_forces
    shots.qm_espxyzs     = qdata.qm_espxyzs
    shots.qm_espvals     = qdata.qm_espvals
    First = True
    if First:
        All = shots
    else:
        All += shots
    return All
Exemplo n.º 3
0
                espval.append(float(s[3]))
            elif len(espxyz) > 0:
                # After reading in a block of ESPs, don't read any more.
                ESPMode = -1 
        if line.strip().startswith("Geometry (in Angstrom)"):
            XMode = 1
            EMode = len(elem) == 0
        if 'Electrostatic Potential' in line.strip() and ESPMode == 0:
            ESPMode = 1
    if len(xyzs) == 0:
        raise Exception('%s has length zero' % psiout)
    return xyzs, elem, espxyz, espval

xyzs, elem, espxyz, espval = read_psi_xyzesp(sys.argv[1])

M = Molecule()
M.xyzs = xyzs
M.elem = elem
M.write('%s.xyz' % os.path.splitext(sys.argv[1])[0])

EM = Molecule()
EM.xyzs = [np.array(espxyz) * 0.52917721092]
EM.elem = ['H' for i in range(len(espxyz))]
EM.write('%s.espx' % os.path.splitext(sys.argv[1])[0], ftype="xyz")

M.qm_espxyzs = EM.xyzs
M.qm_espvals = [np.array(espval)]
M.write("qdata.txt")

np.savetxt('%s.esp' % os.path.splitext(sys.argv[1])[0], espval)
Exemplo n.º 4
0
            elif len(espxyz) > 0:
                # After reading in a block of ESPs, don't read any more.
                ESPMode = -1
        if line.strip().startswith("Geometry (in Angstrom)"):
            XMode = 1
            EMode = len(elem) == 0
        if 'Electrostatic Potential' in line.strip() and ESPMode == 0:
            ESPMode = 1
    if len(xyzs) == 0:
        raise Exception('%s has length zero' % psiout)
    return xyzs, elem, espxyz, espval


xyzs, elem, espxyz, espval = read_psi_xyzesp(sys.argv[1])

M = Molecule()
M.xyzs = xyzs
M.elem = elem
M.write('%s.xyz' % os.path.splitext(sys.argv[1])[0])

EM = Molecule()
EM.xyzs = [np.array(espxyz) * 0.52917721092]
EM.elem = ['H' for i in range(len(espxyz))]
EM.write('%s.espx' % os.path.splitext(sys.argv[1])[0], ftype="xyz")

M.qm_espxyzs = EM.xyzs
M.qm_espvals = [np.array(espval)]
M.write("qdata.txt")

np.savetxt('%s.esp' % os.path.splitext(sys.argv[1])[0], espval)