trjconv can now skip frames

trjconv.py

@@ -9,6 +9,9 @@ num_particles = 0
 step_size = 1
 inp = "trajectory.xyz"
 out = "trjconv.xyz"
+skip = -1
+move = 0
+max_z = 0
 for i, val in enumerate(sys.argv):
     if val == "-dt":
         step_size = int(sys.argv[i+1])
@@ -16,12 +19,21 @@ for i, val in enumerate(sys.argv):
         inp = sys.argv[i+1]
     if val == "-o":
         out = sys.argv[i+1]
+    if val == "-s":
+        skip = int(sys.argv[i+1])
+    if val == "-m":
+        move = float(sys.argv[i+1])
+        max_z = float(sys.argv[i+2])
 
 print "Extracting every %s step from %s" % (step_size, sys.argv[1])
 
 step_counter = 0
 in_step = False
 outfile = open(out, "w")
+
+if skip != -1:
+    print "Skipping %s frames" % skip
+
 with open(inp, "r") as infile:
     for line in infile:
 
@@ -34,8 +46,17 @@ with open(inp, "r") as infile:
         if not line.startswith("atom"):
             step_counter += 1
 
-        if step_counter == 0 or (step_counter % step_size) == 0:
+        if step_counter > skip and step_counter == 0 or (step_counter % step_size) == 0:
-             outfile.write(line)
+             if move > 0 and line.startswith("atom"):
+                split = line.split()
+                split[3] = float(split[3]) + move
+                if(split[3] > max_z):
+                    split[3] -= max_z
+                if(split[3] < 0):
+                    split[3] += max_z
+                outfile.write("%s %s %s %s\n" % (split[0],split[1],split[2],split[3]))
+             else:
+                outfile.write(line)
 
         if step_counter % 100 == 0:
             print(step_counter)