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fwang2011

金虫 (小有名气)

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[资源] cclib 处理大于100个原子的系统 (GAMESS, parser)

前段时间自己遇到的问题，cclib处理大于100个原子的系统出错。

下面是俺的处理方法，共享：
Here is the root problem: cclib (the current released version) cannot parse the log file of system with natom >= 100.

In the log file for the Eigenvalues/MOs:
518  H 98  S -0.000000 0.000000  -0.000000  -0.000000  -0.000000
  519  C 99  S -0.000000 0.000000  -0.000000  -0.000000  -0.000000
  520  C 99  S -0.000000 0.000000  -0.000000  -0.000000  -0.000000
  521  C 99  X -0.000000 0.000000  -0.000000  -0.000000  -0.000000
  522  C 99  Y -0.000000 0.000000  -0.000000  -0.000000  -0.000000
  523  C 99  Z -0.000000 0.000000  -0.000000  -0.000000  -0.000000
  524  H  0  S -0.000000 0.000000  -0.000000  -0.000000  -0.000000
  525  H  1  S -0.000000 0.000000  -0.000000  -0.000000  -0.000000
  526  C  2  S -0.000000 0.000000  -0.000000  -0.000000  -0.000000

The number of atoms are recorded as 0, 1, ...,  instead of 100/200/..., 101/201/..., which is however problematic in calculating CSPA.

My resolution is: introducing a switch to monitor this change. The corresponding code, in gamessparser.py is partially copied in the following:

LINE 714:
            p = re.compile("(\d+)\s*([A-Z][A-Z]?)\s*(\d+)\s*([A-Z]+)"

            oldatom ='0'
            i_atom = 0    #couter to translate to 0s to some hundreds, by C.W.
            flag_w = True #Flag to whether
            for i in range(self.nbasis):
                  line = inputfile.next()

                  # If line is empty, break (ex. for FMO in exam37).
                  if not line.strip(): break

                  # Fill atombasis and aonames only first time around
                  if readatombasis and base == 0:
                     aonames = []
                     start = line[:17].strip()
                     m = p.search(start)
                     if m:
                        g = m.groups()
                        g2 = int(g[2])  #atom index from GAMESS's log file
                        if g2 == 0 and flag_w:                   #c.w.
                              i_atom = i_atom + 100          #c.w
                              flag_w = False
                        if g2 != 0:
                              flag_w = True
                        g2 = g2 + i_atom          #c.w.
                        aoname = "%s%s_%s" % (g[1].capitalize(), str(g2), g[3])    #c.w.
                        #  aoname = "%s%s_%s" % (g[1].capitalize(), g[2], g[3])
                        oldatom = str(g2) #c.w.
                        atomno = g2 - 1    #c.w.
                     # oldatom = g[2]
                     #  atomno = int(g[2])-1
                        orbno = int(g[0])-1

                     else: # For F orbitals, as shown above
                        g = [x.strip() for x in line.split()]
                        g2 = int(g[2])  #atom index from GAMESS's log file
                        if g2 == 0 and flag_w:                   #c.w.
                              i_atom = i_atom + 100          #c.w.
                              flag_w = False                #c.w.
                        if g2 != 0: #c.w.
                              flag_w = True          #c.w.
                        g2 = g2 + i_atom          #c.w.
                        # aoname = "%s%s_%s" % (g[1].capitalize(), oldatom, g[2])
                        aoname = "%s%s_%s" % (g[1].capitalize(), oldatom, str(g2))
                        atomno = int(oldatom)-1
                        orbno = int(g[0])-1
                     self.atombasis[atomno].append(orbno)
                     self.aonames.append(aoname)
                  coeffs = line[15:] # Strip off the crud at the start.
                  j = 0
                  while j*11+4 < len(coeffs):
                     self.mocoeffs[0][base+j, i] = float(coeffs[j * 11