script to filter trajectories

trjconv.py

@@ -0,0 +1,44 @@
+#!/bin/python
+"""
+Script to shrink tajectories by removing frames
+"""
+
+from os import sys
+
+num_particles = 0
+step_size = 1
+inp = "trajectory.xyz"
+out = "trjconv.xyz"
+for i, val in enumerate(sys.argv):
+    if val == "-dt":
+        step_size = int(sys.argv[i+1])
+    if val == "-f":
+        inp = sys.argv[i+1]
+    if val == "-o":
+        out = sys.argv[i+1]
+
+print "Extracting every %s step from %s" % (step_size, sys.argv[1])
+
+step_counter = 0
+in_step = False
+outfile = open(out, "w")
+with open(inp, "r") as infile:
+    for line in infile:
+
+        # get num particles from first line
+        if not line.startswith("atom") and num_particles == 0:
+            num_particles = int(line.split()[0])
+            print "Particles: %s" % num_particles
+            print ""
+
+        if not line.startswith("atom"):
+            step_counter += 1
+
+        if step_counter == 0 or (step_counter % step_size) == 0:
+             outfile.write(line)
+
+        if step_counter % 100 == 0:
+            print(step_counter)
+            sys.stdout.write("\033[F")
+
+outfile.close()