66 lines
1.7 KiB
Python
66 lines
1.7 KiB
Python
#!/bin/python
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"""
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Script to shrink tajectories by removing frames
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"""
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from os import sys
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num_particles = 0
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step_size = 1
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inp = "trajectory.xyz"
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out = "trjconv.xyz"
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skip = -1
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move = 0
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max_z = 0
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for i, val in enumerate(sys.argv):
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if val == "-dt":
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step_size = int(sys.argv[i+1])
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if val == "-f":
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inp = sys.argv[i+1]
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if val == "-o":
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out = sys.argv[i+1]
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if val == "-s":
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skip = int(sys.argv[i+1])
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if val == "-m":
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move = float(sys.argv[i+1])
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max_z = float(sys.argv[i+2])
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print "Extracting every %s step from %s" % (step_size, sys.argv[1])
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step_counter = 0
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in_step = False
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outfile = open(out, "w")
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if skip != -1:
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print "Skipping %s frames" % skip
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with open(inp, "r") as infile:
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for line in infile:
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# get num particles from first line
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if not line.startswith("atom") and num_particles == 0:
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num_particles = int(line.split()[0])
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print "Particles: %s" % num_particles
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print ""
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if not line.startswith("atom"):
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step_counter += 1
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if step_counter > skip and step_counter == 0 or (step_counter % step_size) == 0:
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if move > 0 and line.startswith("atom"):
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split = line.split()
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split[3] = float(split[3]) + move
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if(split[3] > max_z):
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split[3] -= max_z
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if(split[3] < 0):
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split[3] += max_z
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outfile.write("%s %s %s %s\n" % (split[0],split[1],split[2],split[3]))
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else:
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outfile.write(line)
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if step_counter % 100 == 0:
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print(step_counter)
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sys.stdout.write("\033[F")
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outfile.close()
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