A script converting Molpro output file to NMD format file

molpro2nmd.py

@@ -0,0 +1,131 @@
+#!/bin/env python
+import sys, getopt, os, re, cStringIO
+
+filename=sys.argv[1]
+if filename=="":
+    exit("ERROR: INPUT FILE NEEDED.")
+f=open(filename)
+lines=f.readlines()
+
+xyzstart=0
+nmstart=0
+nmistart=0
+nmlstart=0
+
+xyzend=len(lines)
+nmend=len(lines)
+nmiend=len(lines)
+nmlend=len(lines)
+for i in range(0,len(lines)):
+    if lines[i]== " Current geometry (xyz format, in Angstrom)\n": 
+        xyzstart=i
+        break
+else:
+    exit()
+for i in range(xyzstart,len(lines)):
+    if lines[i]== " Normal Modes\n": 
+        nmstart=i
+        break
+else:
+    exit()
+for i in range(xyzstart,len(lines)):
+    if lines[i]== " Normal Modes of imaginary frequencies\n": 
+        nmistart=i
+        nmend=i
+        break
+for i in range(xyzstart,len(lines)):
+    if lines[i]== " Normal Modes of low/zero frequencies\n": 
+        nmlstart=i
+        nmiend=i
+        if nmistart==0 : 
+            nmend=i
+        break
+for i in range(xyzstart,len(lines)):
+    if lines[i].find("Zero point energy:")!=-1:
+        nmlend=i
+        break
+#print xyzstart, nmstart, nmistart, nmlstart
+
+natoms=int(lines[xyzstart+2].split()[0])
+atoms=[]
+coord=[]
+for line in lines[xyzstart+4:xyzstart+4+natoms]:
+    words=line.split()
+    #print line
+    atoms.append(line.split()[0])
+    coord.append(words[1])
+    coord.append(words[2])
+    coord.append(words[3])
+
+modes=[]
+for i in range(0,natoms*natoms*9):
+    modes.append("")
+
+#while True:
+j=0
+if nmistart!=0:
+    for i in range(nmistart, nmiend):
+    #for m in range(1,10):
+        line=lines[i]
+        if not line: break
+        if line[0]!="\n":
+            words=line[:-1].split()
+            if words[0].find("G")!=-1:
+                if words[0]=="GX1":
+                    k=0
+                for l in range(1,len(words)):
+                    #print j ,l ,k 
+                    modes[(j+l-1)*natoms*3+k]=words[l]
+                k=k+1
+                if words[0]=="GZ"+"%d"%natoms:
+                    j=j+len(words)-1
+
+
+#print nmlstart, nmlend, j, natoms
+for i in range(nmlstart, nmlend):
+#for m in range(1,10):
+    line=lines[i]
+    if not line: break
+    if line[0]!="\n":
+        words=line[:-1].split()
+        if words[0].find("G")!=-1:
+            if words[0]=="GX1":
+                k=0
+            for l in range(1,len(words)):
+                #print j ,l ,k 
+                modes[(j+l-1)*natoms*3+k]=words[l]
+            k=k+1
+            if words[0]=="GZ"+"%d"%natoms:
+                j=j+len(words)-1
+
+for i in range(nmstart, nmend):
+#for m in range(1,10):
+    line=lines[i]
+    if not line: break
+    if line[0]!="\n":
+        words=line[:-1].split()
+        if words[0].find("G")!=-1:
+            if words[0]=="GX1":
+                k=0
+            for l in range(1,len(words)):
+                modes[(j+l-1)*natoms*3+k]=words[l]
+            k=k+1
+            if words[0]=="GZ"+"%d"%natoms:
+                j=j+len(words)-1
+# print j
+#quit()
+print "coordinates ",
+for i in range(0,natoms*3):
+    print coord[i],
+print
+
+print "atomnames",
+for i in range(0,natoms):
+    print atoms[i],
+print
+
+for i in range(0,natoms*3):
+    print "mode ",i,
+    for j in range(0,natoms):
+        print modes[i*natoms*3+j*3+0], modes[i*natoms*3+j*3+1], modes[i*natoms*3+j*3+2],
+    print