update 11172014

examples/02_gaussian_split_basis_set/pt10_cl.gjf

@@ -0,0 +1,48 @@
+%nprocshared=12
+# opt=modredundant SCF=QC b3lyp/gen PSEUDO=READ
+
+Title Card Required
+
+-1 1
+ Pt                 5.77400000    7.75900000    3.78900000
+ Pt                 7.75900000    5.77400000    3.78900000
+ Pt                 9.74400000    3.78900000    3.78900000
+ Pt                 5.77400000    9.74400000    1.80400000
+ Pt                 7.75900000    7.75900000    1.80400000
+ Pt                 9.74400000    5.77400000    1.80400000
+ Pt                11.72900000    3.78900000    1.80400000
+ Pt                 7.75900000    9.74400000   -0.18100000
+ Pt                 9.74400000    7.75900000   -0.18100000
+ Pt                11.72900000    5.77400000   -0.18100000
+ Pt                 9.74400000    9.74400000   -2.16600000
+ Pt                11.72900000    7.75900000   -2.16600000
+ Cl                10.43200000    8.77400000    2.26800000
+
+X  1 F
+X  2 F
+X  3 F
+X  4 F
+X  5 F
+X  6 F
+X  7 F
+X  8 F
+X  9 F
+X 10 F
+X 11 F
+X 12 F
+X 13 F
+
+Pt
+lanL2DZ
+****
+Cl
+6-311+g(d,p)
+****
+
+Pt 0
+LANL2DZ
+
+
+
+
+

examples/03_xyz2cfg/lammps_input

@@ -0,0 +1,17 @@
+
+units          real
+atom_style     charge
+boundary       p p p
+
+read_data      lammps.data
+
+dump                    1 all custom 1 dump.lammpstrj id type x y z vx vy vz
+dump_modify             1 sort id
+dump                    101 all cfg 1 dump.*.cfg mass type xs ys zs vx vy vz fx fy fz
+dump_modify             101 element Li Cl S O P
+
+log             rerun.log
+
+#--------Simulation--------
+rerun           movie.xyz dump x y z box no format xyz
+

lib/cfg.py

@@ -0,0 +1,67 @@
+"""cfg file
+"""
+
+from mytype import System, Molecule, Atom
+
+class Cfg(filename):
+    """cfg file
+    """
+    def __init__(self, filename):
+        self.name = ""
+        self.pbc = []
+        self.a = []
+        self.b = []
+        self.c = []
+        self.read(filename)
+        self.natoms = 0
+
+    def read(self, filename):
+        """ read data from cfg file
+        """
+        if filename.endswith(".cfg"):
+            self.name = filename[:-4]
+        else:
+            self.name = filename
+
+        f = open(filename, "r")
+        self.natoms = int(f.readline().strip().split("=")[-1])
+        f.readline() # unit
+        for i in range(3):
+            tokens = i.strip().split("=")[-1].split()[0]
+            self.a.append(float(tokens))
+        for i in range(3):
+            tokens = i.strip().split("=")[-1].split()[0]
+            self.b.append(float(tokens))
+        for i in range(3):
+            tokens = i.strip().split("=")[-1].split()[0]
+            self.c.append(float(tokens))
+        f.readline() # not sure the meaning of the line
+        n = int(f.readline().strip().split("=")[-1])
+        for i in range(n -3):
+            f.readline()
+
+        counter = 0
+        for i in range(self.natoms):
+            if counter % 3 == 0:
+                tokens = []
+            tokens.append(i.strip().split())
+            self.coords.append(token)
+            counter += 1
+
+    def parser(self,):
+        """ parse cfg to system
+        """
+        s = System()
+        s.pbc = v2lattice(a, b, c)
+        s.natoms = self.natoms
+        for i in range(s.natoms):
+            atom = Atom()
+            atom.name = self.coords[i][1][0]
+            x = float(self.coords[i][2][0])
+            y = float(self.coords[i][2][1])
+            z = float(self.coords[i][2][2])
+            atom.x[0] = a[0]*x + b[0]*y + c[0]*z
+            atom.x[1] = a[1]*x + b[1]*y + c[1]*z
+            atom.x[2] = a[2]*x + b[2]*y + c[2]*z
+            s.atoms.append(atom)
+

tools/Lammps/vidcompress

@@ -0,0 +1,24 @@
+#!/bin/sh
+# see http://www.cscs.ch/~mvalle/mencoder/mencoder.html
+
+# touch ~/.mplayer/mencoder #
+
+JPEG_DIR=Jpg
+MPG_FILE=AtomEye.mpg
+
+jpgfile=`ls $JPEG_DIR/ | grep --max-count=1 -i .jpg`
+
+geometry=`identify -verbose $JPEG_DIR/$jpgfile | grep Geometry | cut -d: -f2`
+
+height=`echo $geometry | cut -dx -f1`
+width=`echo $geometry | cut -dx -f2`
+
+optimal_bitrate=`echo "scale=0; 50 * 25 * $width * $height / 256" | bc -l`
+
+rm -f $MPG_FILE
+
+opt="vbitrate=$optimal_bitrate:mbd=2:keyint=132:vqblur=1.0:cmp=2:subcmp=2:dia=2:last_pred=3"
+
+mencoder -ovc lavc -lavcopts vcodec=msmpeg4v2:vpass=1:$opt -mf type=jpg:fps=8 -nosound -o /dev/null mf://$JPEG_DIR/\*.jpg
+
+mencoder -ovc lavc -lavcopts vcodec=msmpeg4v2:vpass=2:$opt -mf type=jpg:fps=8 -nosound -o $MPG_FILE mf://$JPEG_DIR/\*.jpg

tools/hun/plot_fragtable.py

@@ -70,8 +70,15 @@
     if not os.path.exists("frag_details"):
         os.mkdir("frag_details")
     os.chdir("frag_details")
-    tmp = np.array([data[0], data[i]])
-    np.savetxt(head[i] + ".dat", tmp)
+    if (0):
+        tmp = np.array([data[0], data[i]])
+        np.savetxt(head[i] + ".dat", tmp)
+    if (1):
+        o = open(head[i] + ".csv", "w")
+        for j in range(len(data[0])):
+            if j%1 == 0:
+                o.write("%.4f, %.4f\n"%(data[0][j], data[i][j]))
+        o.close()
     os.chdir("..")
 
 #plot the temperature

tools/vasp/get_potcar.py

@@ -24,7 +24,7 @@
 POT = {"N":"N", "O":"O", "H":"H", "C":"C", "Li":"Li", "S":"S", "Ti":"Ti", "P":"P", 
        "Ca":"Ca_pv", "Al":"Al", "Cu":"Cu", "Na":"Na", "Cl":"Cl", "Cr":"Cr", "Ga":"Ga",
         "Br":"Br", "D": "H", "Si": "Si", "Ni": "Ni", "Pt":"Pt"}
-POT_DATA_BASE = "/project/source/VASP/vasp.5.2/potcar/potpaw_PBE"
+POT_DATA_BASE = "/project/source/VASP/vasp.5.3.5/potcar/potpaw_PBE"
 
 o = open("POTCAR", "w")
 a = Poscar("POSCAR")