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138 lines
4.3 KiB
Python
138 lines
4.3 KiB
Python
#!/usr/bin/python
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# Script: block.py
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# Purpose: thermodynamic block averages from LAMMPS log files
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# Syntax: block.py nblocks nskip log.1 log.2 ...
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# nblocks = number of blocks for block averages
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# nskip = skip first nskip samples in the log file(s)
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# files = series of log files (LAMMPS thermo one style only)
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# Example: block.py 10 0 log.*
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# Author: Paul Crozier (Sandia)
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# enable script to run from Python directly w/out Pizza.py
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import sys
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from log import log
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if not globals().has_key("argv"): argv = sys.argv
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# main script
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if len(argv) < 4:
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raise StandardError, "Syntax: block.py nblocks nskip log.1 log.2 ..."
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nblocks = int(argv[1])
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nskip = int(argv[2])
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files = ' '.join(argv[3:])
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l = log(files)
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# assumes LAMMPS thermo style one
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e_bond,e_pair,e_total,pressure,step,temperature = \
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l.get("E_bond","E_pair", "E_total", "Pressure", "Step", "Temperature")
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if "Volume" in l.names:
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vflag = 1
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volume = l.get("Volume")
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else: vflag = 0
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print "Computing %g block averages" % nblocks
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print "Skipping first %g samples" % nskip
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n = len(step)
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n_per_block = (n-nskip)/nblocks
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k = nskip
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temperature_ave = []
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e_bond_ave = []
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e_pair_ave = []
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e_total_ave = []
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pressure_ave = []
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volume_ave = []
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print
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print " Block Samples Temperature E_bond E_pair", \
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" E_total Pressure Volume"
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for i in xrange(nblocks):
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temperature_sum = 0
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e_bond_sum = 0
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e_pair_sum = 0
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e_total_sum = 0
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pressure_sum = 0
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volume_sum = 0
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samples = 0
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for j in xrange(n_per_block):
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temperature_sum += temperature[k]
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e_bond_sum += e_bond[k]
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e_pair_sum += e_pair[k]
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e_total_sum += e_total[k]
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pressure_sum += pressure[k]
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if vflag: volume_sum += volume[k]
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samples += 1
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k += 1
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temperature_ave.append(temperature_sum/samples)
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e_bond_ave.append(e_bond_sum/samples)
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e_pair_ave.append(e_pair_sum/samples)
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e_total_ave.append(e_total_sum/samples)
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pressure_ave.append(pressure_sum/samples)
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volume_ave.append(volume_sum/samples)
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print " %5i %10i %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \
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(i+1, samples, temperature_ave[i], e_bond_ave[i], e_pair_ave[i], \
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e_total_ave[i], pressure_ave[i], volume_ave[i])
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grand_ave_temperature = 0.0
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grand_ave_e_bond = 0.0
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grand_ave_e_pair = 0.0
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grand_ave_e_total = 0.0
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grand_ave_pressure = 0.0
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grand_ave_volume = 0.0
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stdev_temperature = 0.0
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stdev_e_bond = 0.0
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stdev_e_pair = 0.0
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stdev_e_total = 0.0
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stdev_pressure = 0.0
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stdev_volume = 0.0
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for i in xrange(nblocks):
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grand_ave_temperature += temperature_ave[i]
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grand_ave_e_bond += e_bond_ave[i]
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grand_ave_e_pair += e_pair_ave[i]
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grand_ave_e_total += e_total_ave[i]
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grand_ave_pressure += pressure_ave[i]
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grand_ave_volume += volume_ave[i]
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grand_ave_temperature /= nblocks
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grand_ave_e_bond /= nblocks
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grand_ave_e_pair /= nblocks
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grand_ave_e_total /= nblocks
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grand_ave_pressure /= nblocks
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grand_ave_volume /= nblocks
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for i in xrange(nblocks):
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stdev_temperature += (temperature_ave[i] - grand_ave_temperature)* \
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(temperature_ave[i] - grand_ave_temperature)
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stdev_e_bond += (e_bond_ave[i] - grand_ave_e_bond)* \
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(e_bond_ave[i] - grand_ave_e_bond)
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stdev_e_pair += (e_pair_ave[i] - grand_ave_e_pair)* \
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(e_pair_ave[i] - grand_ave_e_pair)
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stdev_e_total += (e_total_ave[i] - grand_ave_e_total)* \
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(e_total_ave[i] - grand_ave_e_total)
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stdev_pressure += (pressure_ave[i] - grand_ave_pressure)* \
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(pressure_ave[i] - grand_ave_pressure)
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stdev_volume += (volume_ave[i] - grand_ave_volume)* \
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(volume_ave[i] - grand_ave_volume)
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from math import *
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stdev_temperature = sqrt(stdev_temperature/(nblocks-1))
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stdev_e_bond = sqrt(stdev_e_bond/(nblocks-1))
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stdev_e_pair = sqrt(stdev_e_pair/(nblocks-1))
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stdev_e_total = sqrt(stdev_e_total/(nblocks-1))
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stdev_pressure = sqrt(stdev_pressure/(nblocks-1))
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stdev_volume = sqrt(stdev_volume/(nblocks-1))
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print " ====================================================", \
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"==================================="
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print " Ave. %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \
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(grand_ave_temperature, grand_ave_e_bond, grand_ave_e_pair, \
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grand_ave_e_total, grand_ave_pressure, grand_ave_volume)
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print " Stdev %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \
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(stdev_temperature, stdev_e_bond, stdev_e_pair, \
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stdev_e_total, stdev_pressure, stdev_volume)
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