update

lib/cons.py

@@ -2,7 +2,7 @@
 """
 
 # Atom number - Atom name map
-ELEMENT = {1:"H", 3:"Li", 6:"C", 7:"N",  8:"O", 9:"F", 12: "Mg", 13: "Al", 14:"Si", 
+ELEMENT = {1:"H", 3:"Li", 5:"B", 6:"C", 7:"N",  8:"O", 9:"F", 12: "Mg", 13: "Al", 14:"Si", 
             15:"P", 16:"S", 17:"Cl", 20:"Ca", 22:"Ti", 28:"Ni", 31:"Ga", 32:"Ge"}
 # Atom name - Atom number map
 ELEMENT2ATN = {"H":1, "Li":3, "C":6, "N":7,  "O":8, "F":9, "Na":11, 12: "Mg", "Al":13, "Si":14, 
@@ -11,7 +11,7 @@
                "Ba": 56, "Y":39, "Zr": 40, "Cu": 29, "K":19, "Br":35, "Cs":55, "Ag":47,
                "Ru":44, "He":2, "Au":79, "Cd": 48, "Cr": 24, "Fe": 26, "I": 53, "Mn": 25,
                "Pd": 46, "Rh": 45, "Sc": 21, "Tc": 43, "Zn": 30, "W": 74, "Se": 34, "B": 5,
-               "Mg": 12, "Bi": 83, "Pb": 82, "Ge": 32}
+               "Mg": 12, "Bi": 83, "Pb": 82, "Ge": 32, "Sr":38, "Rb":37}
 
 # Atom name - Atom mass map
 ELEMENT2MASS = {"H": 1.0079, "O": 15.999, "N": 14.007, "Li":6.941, "LI":6.941, "Al": 26.982, "AL": 26.982, 
@@ -27,7 +27,7 @@
                 "He": 4.0026, "Zn": 65.39, "Tc": 98.907, "Sc": 44.956, "Ru": 101.07, "Rh": 102.906,
                 "Pd": 106.42, "Mn": 54.938, "Cr": 51.996, "Cd": 112.411, "B": 10.811,
                 "Ru": 101.07, "RU":101.07, "W": 183.84, "Se": 78.96, "SE": 78.96, "Ir":192.22,
-                "Pb": 207.20}
+                "Pb": 207.20, "Sr":87.62, "Rb":85.468}
 # Atom name - Atom mass map
 MASS2ELMENT = {1.0079: "H",12.011: "C", 14.0067:"N", 15.9994: "O", 24: "Mg",  27: "Al", 28:"Si", 
                                         14.0070:"N", 15.9990: "O", 

lib/g03.py

@@ -151,7 +151,7 @@ def read(self, filename):
         f.close()
 
     def __parse_keyword(self,):
-	keywords = []
+        keywords = []
         tmp = ''
         state = 0
         for i in self.methods:
@@ -233,7 +233,7 @@ def getEnergy(self, ):
                 if "HF" in i:
                     ener = float(i[3:])
         else:
-            print "Error: No energy read"
+            print("Error: No energy read")
 
         # get the zpe energy
         zpe = 0
@@ -245,14 +245,14 @@ def getEnergy(self, ):
         f.close()
         return ener, zpe
 
-    def getCharge(self,):
+    def getMullikenCharge(self,):
         """get Mulliken charege from QM
         """
         charges = []
         lines = []
         f = open(self.name, "r")
         for i in f:
-            if "Mulliken atomic charges" in i or \
+            if "Mulliken charges" in i or \
                 "Total atomic charges" in i:
                 break
         for i in f:
@@ -265,9 +265,29 @@ def getCharge(self,):
             charges.append(tokens)
         return charges
 
+    def getESPCharge(self,):
+        """get ESP charege from QM
+        """
+        charges = []
+        lines = []
+        f = open(self.name, "r")
+        for i in f:
+            if "ESP charges" in i or \
+                "Total atomic charges" in i:
+                break
+        for i in f:
+            if "Sum of ESP charges" in i:
+                break
+            lines.append(i)
+        f.close()
+        for i in lines[1:]:
+            tokens = i.strip().split()
+            charges.append(tokens)
+        return charges
+
 def main():                
     if len(sys.argv) < 2:
-        print "g03.py logfile"
+        print("g03.py logfile")
     else:
         for i in sys.argv[1:]:
             geo = i.split(".")[0]

lib/itp.py

@@ -0,0 +1,95 @@
+import sys
+import copy
+import os
+import time
+
+def usage():
+    print("""xxxxx
+xxxxxxxxxxxxxxxxxxx
+xxxxxxxxxxxxxxxxxxxxxx
+""")
+
+def parseItpfile(itpfile):
+    parms = {}
+    term =''
+    f = open(itpfile, 'r')
+    for i in f:
+        if i.startswith('#') or i.startswith(';'):
+            pass
+        elif len(i.strip()) < 1:
+            pass
+        elif i.startswith('['):
+            term = i.split()[1]
+            if not term in parms:
+                parms[term] = []
+        else:
+            if term !='':
+                clear_comments = 1
+                if clear_comments:
+                    if ';' in i:
+                        parms[term].append(i.split(';')[0].split())
+                    else:
+                        parms[term].append(i.split())
+    f.close()
+    return parms
+
+def writeItp(itpfile, parms):
+    o = open(itpfile, 'w')
+    ISOTIMEFORMAT='%Y-%m-%d %X'
+    currentTime = time.strftime( ISOTIMEFORMAT, time.localtime( time.time() ) )
+    #o.write("#CREATED AT%s\n\n"%currentTime)
+
+    sections = ['moleculetype', 'atoms', 'bonds', 'angles', 'dihedrals']
+    for i in sections:
+        if i in parms.keys():
+            o.write("[ %s ]\n"%i)
+            for ii in parms[i]:
+                line = ''
+                for iii in ii:
+                    line += iii + ' '
+                line += '\n'
+                o.write(line)
+    o.close()
+
+def parmModify(parm, deltaS,epsilonS, term, atomtype):
+    parmM = {}
+    for (i,j) in parm.items():
+        parmM[i] = parm[i]
+    parmM[term] = []
+    for j in parm[term]:
+        m = copy.copy(j)
+        if j[0] == atomtype:
+            m[4] = "%.4f"%(float(j[4])*deltaS/100)
+            m[5] = "%.4f"%(float(j[5])*epsilonS/100)
+        parmM[term].append(m)
+    return parmM
+
+def scanAll(parm, itpfile):
+    folder = os.getcwd()
+    term = "atomtypes"
+    atom = []
+    for i in parm[term]:
+        atom.append(i[0])
+    delta = [105, 100, 95]
+    epsilon = [120, 100, 80]
+    for a in atom:
+        for i in delta:
+            for j in epsilon:
+                fullname = os.path.join(folder,'%s_%03d_%03d'%(a,i,j))
+                parmM = parmModify(parm, i,j, term, a)
+                if os.path.isdir(fullname):
+                    pass
+                else:
+                    os.system("mkdir %s"%fullname)
+                os.system("cp run.gro run.mdp *.top grompp.sh %s"%fullname)
+                outitpfile = os.path.join(fullname, itpfile)
+                writeItp(outitpfile, parmM)
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        usage()
+    else:
+        itpfile = sys.argv[1]
+        parmOr = parseItpfile(itpfile)
+        writeItp('test.itp', parmOr)
+        #scanAll(parmOr, itpfile)

lib/output_conf.py

@@ -345,7 +345,7 @@ def toPoscar(system, outfile="POSCAR"):
     s = system
     o = open(outfile, "w")
     ndx = open(ndxfile, 'w')
-    ndx.write('# original-id new-id\n')
+    ndx.write('# new-id old-id\n')
     o.write("%s\n"%s.name) 
     o.write("%20.15f\n"%s.scaleFactor)
 
@@ -396,7 +396,7 @@ def toPoscar(system, outfile="POSCAR"):
             natom += 1
 
     for i in range(natom):
-        ndx.write('%d %d\n'%(i+1, id_numbers[i]))
+        ndx.write('%d %d\n'%(id_numbers[i], i+1))
         xf = coords[i][0]
         yf = coords[i][1]
         zf = coords[i][2]

molecules/ase/get_mol.py

@@ -0,0 +1,8 @@
+from ase.build import molecule
+from ase.collections import g2
+from ase.io import write
+
+for i in g2.names:
+    atoms = molecule(i)
+    write(i+'.pdb', atoms)
+

tools/rdkit/mol2xyz.py

@@ -8,13 +8,14 @@
 n_atoms = int(tokens[0])
 
 coords = []
-for i in range(4, 4+n_atoms):
+for i in range(len(lines)):
     tokens = lines[i].strip().split()
-    line = '%s %s %s %s\n'%(tokens[3], tokens[0], tokens[1], tokens[2])
-    coords.append(line)
+    if len(tokens) == 16:
+        line = '%s %s %s %s\n'%(tokens[3], tokens[0], tokens[1], tokens[2])
+        coords.append(line)
 
 o = open('%s.xyz'%sys.argv[1], 'w')
-o.write('%d\n\n'%n_atoms)
+o.write('%d\n\n'%len(coords))
 for i in coords:
     o.write(i)
 o.close()

tools/vasp/get_potcar.py

@@ -92,8 +92,6 @@
     POT_DATA_BASE = "/p/home/taocheng/src/vasp/vasp.5.3/potcar/potpaw_PBE"
 elif socket.gethostname() == "tao-ThinkCentre-M79":
     POT_DATA_BASE = "/home/tao/src/vasp/vasp.5.3.5/potcar/potpaw_PBE"
-elif socket.gethostname() == "tao-ThinkCentre-M79":
-    POT_DATA_BASE = "/home/tao/src/vasp/vasp.5.3.5/potcar/potpaw_PBE"
 elif socket.gethostname() == "tao-Precision-Tower-3420-ubuntu":
     POT_DATA_BASE = "/home/tao/data/soft/vasp/vasp.5.3.5/potcar/potpaw_PBE"
 elif socket.gethostname() == "mu05":