Committer: ckloss <ckloss@fluid38.(none)>

On branch master
 Initial commit for lpp, version 2011-10-11

scripts/block.py

@@ -0,0 +1,137 @@
+#!/usr/bin/python
+
+# Script:  block.py
+# Purpose: thermodynamic block averages from LAMMPS log files
+# Syntax:  block.py nblocks nskip log.1 log.2 ...
+#          nblocks = number of blocks for block averages 
+#          nskip = skip first nskip samples in the log file(s)
+#          files = series of log files (LAMMPS thermo one style only)
+# Example: block.py 10 0 log.*
+# Author:  Paul Crozier (Sandia)
+
+# enable script to run from Python directly w/out Pizza.py
+
+import sys
+from log import log
+if not globals().has_key("argv"): argv = sys.argv
+
+# main script
+
+if len(argv) < 4:
+  raise StandardError, "Syntax: block.py nblocks nskip log.1 log.2 ..."
+
+nblocks = int(argv[1])
+nskip = int(argv[2])
+files = ' '.join(argv[3:])
+
+l = log(files)
+
+# assumes LAMMPS thermo style one
+
+e_bond,e_pair,e_total,pressure,step,temperature = \
+  l.get("E_bond","E_pair", "E_total", "Pressure", "Step", "Temperature")
+if "Volume" in l.names:
+  vflag = 1
+  volume = l.get("Volume")
+else: vflag = 0
+
+print "Computing %g block averages" % nblocks
+print "Skipping first %g samples" % nskip
+
+n = len(step)
+n_per_block = (n-nskip)/nblocks
+k = nskip
+temperature_ave = []
+e_bond_ave = []
+e_pair_ave = [] 
+e_total_ave = []
+pressure_ave = []
+volume_ave = []
+
+print
+print " Block    Samples Temperature      E_bond      E_pair",  \
+  "    E_total    Pressure      Volume"
+
+for i in xrange(nblocks):
+  temperature_sum = 0
+  e_bond_sum = 0
+  e_pair_sum = 0
+  e_total_sum = 0
+  pressure_sum = 0
+  volume_sum = 0
+  samples = 0
+  for j in xrange(n_per_block): 
+    temperature_sum += temperature[k]
+    e_bond_sum += e_bond[k]
+    e_pair_sum += e_pair[k]
+    e_total_sum += e_total[k]
+    pressure_sum += pressure[k]
+    if vflag: volume_sum += volume[k]
+    samples += 1
+    k += 1
+  temperature_ave.append(temperature_sum/samples)
+  e_bond_ave.append(e_bond_sum/samples)
+  e_pair_ave.append(e_pair_sum/samples)
+  e_total_ave.append(e_total_sum/samples)
+  pressure_ave.append(pressure_sum/samples)
+  volume_ave.append(volume_sum/samples)
+  print " %5i %10i %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" %  \
+    (i+1, samples, temperature_ave[i], e_bond_ave[i], e_pair_ave[i], \
+    e_total_ave[i], pressure_ave[i], volume_ave[i])
+
+grand_ave_temperature = 0.0
+grand_ave_e_bond = 0.0
+grand_ave_e_pair = 0.0
+grand_ave_e_total = 0.0
+grand_ave_pressure = 0.0
+grand_ave_volume = 0.0 
+stdev_temperature = 0.0
+stdev_e_bond = 0.0
+stdev_e_pair = 0.0
+stdev_e_total = 0.0
+stdev_pressure = 0.0
+stdev_volume = 0.0 
+for i in xrange(nblocks):
+  grand_ave_temperature += temperature_ave[i]
+  grand_ave_e_bond += e_bond_ave[i]
+  grand_ave_e_pair += e_pair_ave[i]
+  grand_ave_e_total += e_total_ave[i]
+  grand_ave_pressure += pressure_ave[i]
+  grand_ave_volume += volume_ave[i] 
+grand_ave_temperature /= nblocks
+grand_ave_e_bond /= nblocks
+grand_ave_e_pair /= nblocks
+grand_ave_e_total /= nblocks
+grand_ave_pressure /= nblocks
+grand_ave_volume /= nblocks 
+for i in xrange(nblocks):
+  stdev_temperature += (temperature_ave[i] - grand_ave_temperature)*  \
+                       (temperature_ave[i] - grand_ave_temperature)
+  stdev_e_bond += (e_bond_ave[i] - grand_ave_e_bond)*  \
+                  (e_bond_ave[i] - grand_ave_e_bond)
+  stdev_e_pair += (e_pair_ave[i] - grand_ave_e_pair)*  \
+                  (e_pair_ave[i] - grand_ave_e_pair) 
+  stdev_e_total += (e_total_ave[i] - grand_ave_e_total)*  \
+                   (e_total_ave[i] - grand_ave_e_total)
+  stdev_pressure += (pressure_ave[i] - grand_ave_pressure)*  \
+                    (pressure_ave[i] - grand_ave_pressure)
+  stdev_volume += (volume_ave[i] - grand_ave_volume)*  \
+                  (volume_ave[i] - grand_ave_volume)
+from math import *
+stdev_temperature = sqrt(stdev_temperature/(nblocks-1))
+stdev_e_bond = sqrt(stdev_e_bond/(nblocks-1))
+stdev_e_pair = sqrt(stdev_e_pair/(nblocks-1))
+stdev_e_total = sqrt(stdev_e_total/(nblocks-1))
+stdev_pressure = sqrt(stdev_pressure/(nblocks-1))
+stdev_volume = sqrt(stdev_volume/(nblocks-1)) 
+
+print " ====================================================",  \
+  "==================================="
+  
+print " Ave.             %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \
+    (grand_ave_temperature, grand_ave_e_bond, grand_ave_e_pair, \
+    grand_ave_e_total, grand_ave_pressure, grand_ave_volume)
+    
+print " Stdev            %11.2f %11.2f %11.2f %11.2f %11.2f %11.2f" % \
+    (stdev_temperature, stdev_e_bond, stdev_e_pair, \
+    stdev_e_total, stdev_pressure, stdev_volume)