--- /dev/null 2004-02-18 08:26:44.000000000 -0700
+++ /home/sjplimp/pizza/src/histo.py 2005-12-20 15:06:56.000000000 -0700
@@ -0,0 +1,86 @@
+# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+#
+# Copyright (2005) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+# certain rights in this software. This software is distributed under
+# the GNU General Public License.
+
+# histo tool
+
+oneline = "Particle density histogram from a dump"
+
+docstr = """
+h = histo(d) d = dump/cdump object
+
+x,y = h.compute('x',N,lo,hi) compute histogram in dim with N bins
+
+ lo/hi are optional, if not used histo will be over entire box
+"""
+
+# History
+# 12/05, Steve Plimpton (SNL): original version
+
+# ToDo list
+
+# Variables
+# data = dump object
+
+# Imports and external programs
+
+# Class definition
+
+class histo:
+
+ # --------------------------------------------------------------------
+
+ def __init__(self,data):
+ self.data = data
+
+ # --------------------------------------------------------------------
+
+ def compute(self,dim,nbins,lo=None,hi=None):
+ if dim == 'x': idim = 2
+ elif dim == 'y': idim = 3
+ elif dim == 'z': idim = 4
+ else: raise StandardError,"illegal dim value"
+
+ y = nbins*[0]
+
+ count = 0
+ n = flag = 0
+ while 1:
+ which,time,flag = self.data.iterator(flag)
+ if flag == -1: break
+ time,box,atoms,bonds,tris,lines = self.data.viz(which)
+
+ if not lo:
+ if dim == 'x':
+ lo = box[0]
+ hi = box[3]
+ elif dim == 'y':
+ lo = box[1]
+ hi = box[4]
+ elif dim == 'z':
+ lo = box[2]
+ hi = box[5]
+
+ delta = (hi-lo) / nbins;
+ invdelta = 1.0/delta
+
+ for atom in atoms:
+ coord = atom[idim]
+ ibin = int((coord-lo) * invdelta)
+ if ibin < 0 or ibin >= nbins: continue
+ y[ibin] += 1
+ count += 1
+
+ n += 1
+
+ x = nbins*[0]
+ for i in xrange(nbins): x[i] = (i+0.5)*delta
+
+ print "histogram snapshots = ",n
+ print "histogram counts (per snap) = %d (%g)" % (count,float(count)/n)
+ print "histogram bounds = ",lo,hi
+ return x,y
--- /dev/null 2004-02-18 08:26:44.000000000 -0700
+++ /home/sjplimp/pizza/doc/histo.txt 2005-12-20 15:07:04.000000000 -0700
@@ -0,0 +1,40 @@
+"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c
+
+:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html)
+:link(pd,Manual.html)
+:link(pc,Section_tools.html)
+
+:line
+
+histo tool :h3
+
+[Purpose:]
+
+Particle density histogram from a dump.
+
+[Description:]
+
+The histo tool creates spatial histograms of particle snapshots in
+a dump file.
+
+The histo constructor takes an object that stores atom snapshots
+("dump"_dump.html, "data"_data.html) as its argument.
+
+The compute() method creates a histogram in a specific dimension at a
+desired resolution, averaged across all selected snapshots and atoms
+in the dump. The returned vectors can be plotted; x is the distance
+along the chosen dimension, y is the histogram counts.
+
+[Usage:]
+
+h = histo(d) d = dump/cdump object :pre
+
+x,y = h.compute('x',N,lo,hi) compute histogram in dim with N bins :pre
+
+ lo/hi are optional, if not used histo will be over entire box :pre
+
+[Related tools:]
+
+"dump"_dump.html
+
+[Prerequisites:] none
--- /dev/null 2004-02-18 08:26:44.000000000 -0700
+++ /home/sjplimp/pizza/doc/histo.html 2005-12-20 15:08:32.000000000 -0700
@@ -0,0 +1,45 @@
+
+Pizza.py WWW Site - Pizza.py Documentation - Pizza.py Tools
+
+
+
+
+
+
+
+
+
+histo tool
+
+Purpose:
+
+Particle density histogram from a dump.
+
+Description:
+
+The histo tool creates spatial histograms of particle snapshots in
+a dump file.
+
+The histo constructor takes an object that stores atom snapshots
+(dump, data) as its argument.
+
+The compute() method creates a histogram in a specific dimension at a
+desired resolution, averaged across all selected snapshots and atoms
+in the dump. The returned vectors can be plotted; x is the distance
+along the chosen dimension, y is the histogram counts.
+
+Usage:
+
+h = histo(d) d = dump/cdump object
+
+x,y = h.compute('x',N,lo,hi) compute histogram in dim with N bins
+
+ lo/hi are optional, if not used histo will be over entire box
+
+Related tools:
+
+dump
+
+Prerequisites: none
+
+
--- /home/sjplimp/oldpizza/doc/Section_tools.txt 2005-11-07 17:10:41.000000000 -0700
+++ /home/sjplimp/pizza/doc/Section_tools.txt 2005-12-20 15:08:24.000000000 -0700
@@ -25,7 +25,7 @@
File conversion: pdb, vtk, xyz
GUI wrappers: animate, image, plotview, vcr
Plotting: gnu, matlab
-Miscellaneous: pair, vec :tb(s=:)
+Miscellaneous: histo, pair, vec :tb(s=:)
Within the plotting and viz categories, individual tools share many
common methods, so the tools can often be used interchangeably. For
@@ -43,6 +43,7 @@
"dump.py"_dump.html; Read, write, manipulate LAMMPS dump files and atom attributes
"gl.py"_gl.html; 3d interactive visualization via OpenGL
"gnu.py"_gnu.html; Create plots via "GnuPlot"_gnuplot plotting program
+"histo.py"_histo.html; Particle density histogram from a dump
"image.py"_image.html; View and manipulate images
"log.py"_log.html; Read LAMMPS log files and extract thermodynamic data
"matlab.py"_matlab.html; Create plots via "MatLab"_matlab numerical analysis program
--- /home/sjplimp/oldpizza/doc/Section_tools.html 2005-11-07 17:10:41.000000000 -0700
+++ /home/sjplimp/pizza/doc/Section_tools.html 2005-12-20 15:08:32.000000000 -0700
@@ -29,7 +29,7 @@
| File conversion | pdb, vtk, xyz |
| GUI wrappers | animate, image, plotview, vcr |
| Plotting | gnu, matlab |
-| Miscellaneous | pair, vec
+ |
| Miscellaneous | histo, pair, vec
|
Within the plotting and viz categories, individual tools share many
@@ -49,6 +49,7 @@
| dump.py | Read, write, manipulate LAMMPS dump files and atom attributes |
| gl.py | 3d interactive visualization via OpenGL |
| gnu.py | Create plots via GnuPlot plotting program |
+| histo.py | Particle density histogram from a dump |
| image.py | View and manipulate images |
| log.py | Read LAMMPS log files and extract thermodynamic data |
| matlab.py | Create plots via MatLab numerical analysis program |
--- /home/sjplimp/oldpizza/doc/Manual.txt 2005-11-07 17:10:41.000000000 -0700
+++ /home/sjplimp/pizza/doc/Manual.txt 2005-12-20 15:07:56.000000000 -0700
@@ -69,6 +69,8 @@
"Extending Pizza.py"_Section_extend.html :l
:ole
+:line
+
List of tools in Pizza.py:
"animate.py"_animate.html; Animate a series of image files
@@ -77,6 +79,7 @@
"dump.py"_dump.html; Read, write, manipulate LAMMPS dump files and atom attributes
"gl.py"_gl.html; 3d interactive visualization via OpenGL
"gnu.py"_gnu.html; Create plots via "GnuPlot"_gnuplot plotting program
+"histo.py"_histo.html; Particle density histogram from a dump
"image.py"_image.html; View and manipulate images
"log.py"_log.html; Read LAMMPS log files and extract thermodynamic data
"matlab.py"_matlab.html; Create plots via "MatLab"_matlab numerical analysis program
--- /home/sjplimp/oldpizza/doc/Manual.html 2005-11-07 17:10:41.000000000 -0700
+++ /home/sjplimp/pizza/doc/Manual.html 2005-12-20 15:08:32.000000000 -0700
@@ -95,6 +95,8 @@
+
+
List of tools in Pizza.py:
@@ -104,6 +106,7 @@
| dump.py | Read, write, manipulate LAMMPS dump files and atom attributes |
| gl.py | 3d interactive visualization via OpenGL |
| gnu.py | Create plots via GnuPlot plotting program |
+| histo.py | Particle density histogram from a dump |
| image.py | View and manipulate images |
| log.py | Read LAMMPS log files and extract thermodynamic data |
| matlab.py | Create plots via MatLab numerical analysis program |
--- /dev/null 2004-02-18 08:26:44.000000000 -0700
+++ /home/sjplimp/pizza/examples/test_histo.py 2005-12-20 15:11:09.000000000 -0700
@@ -0,0 +1,13 @@
+# simple test of histo tool
+# requires files/dump.kinase
+
+d = dump("files/dump.kinase")
+h = histo(d)
+x,y = h.compute('x',25)
+g = gnu()
+g.xtitle("X position")
+g.ytitle("Particle Count")
+g.title("Histogram of Particle Density")
+g.plot(x,y)
+
+print "all done ... type CTRL-D to exit Pizza.py"