Merge branch 'lammps:develop' into mliappy_unified
This commit is contained in:
Steven Anaya
File diff suppressed because it is too large
Load Diff
1
python/examples/pizza/dump.py
Symbolic link
1
python/examples/pizza/dump.py
Symbolic link
@ -0,0 +1 @@
|
||||
../../../tools/python/pizza/dump.py
|
||||
@ -1,390 +0,0 @@
|
||||
# Pizza.py toolkit, https://lammps.github.io/pizza
|
||||
# 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.
|
||||
|
||||
# for python3 compatibility
|
||||
from __future__ import print_function
|
||||
|
||||
# gnu tool
|
||||
|
||||
oneline = "Create plots via GnuPlot plotting program"
|
||||
|
||||
docstr = """
|
||||
g = gnu() start up GnuPlot
|
||||
g.stop() shut down GnuPlot process
|
||||
|
||||
g.plot(a) plot vector A against linear index
|
||||
g.plot(a,b) plot B against A
|
||||
g.plot(a,b,c,d,...) plot B against A, D against C, etc
|
||||
g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc
|
||||
|
||||
each plot argument can be a tuple, list, or Numeric/NumPy vector
|
||||
mplot loops over range(M,N,S) and create one plot per iteration
|
||||
last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors
|
||||
each plot is made from a portion of the vectors, depending on loop index i
|
||||
Ith plot is of b[0:i] vs a[0:i], etc
|
||||
series of plots saved as file0000.eps, file0001.eps, etc
|
||||
if use xrange(),yrange() then plot axes will be same for all plots
|
||||
|
||||
g("plot 'file.dat' using 2:3 with lines") execute string in GnuPlot
|
||||
|
||||
g.enter() enter GnuPlot shell
|
||||
gnuplot> plot sin(x) with lines type commands directly to GnuPlot
|
||||
gnuplot> exit, quit exit GnuPlot shell
|
||||
|
||||
g.export("data",range(100),a,...) create file with columns of numbers
|
||||
|
||||
all vectors must be of equal length
|
||||
could plot from file with GnuPlot command: plot 'data' using 1:2 with lines
|
||||
|
||||
g.select(N) figure N becomes the current plot
|
||||
|
||||
subsequent commands apply to this plot
|
||||
|
||||
g.hide(N) delete window for figure N
|
||||
g.save("file") save current plot as file.eps
|
||||
|
||||
Set attributes for current plot:
|
||||
|
||||
g.erase() reset all attributes to default values
|
||||
g.aspect(1.3) aspect ratio
|
||||
g.xtitle("Time") x axis text
|
||||
g.ytitle("Energy") y axis text
|
||||
g.title("My Plot") title text
|
||||
g.title("title","x","y") title, x axis, y axis text
|
||||
g.xrange(xmin,xmax) x axis range
|
||||
g.xrange() default x axis range
|
||||
g.yrange(ymin,ymax) y axis range
|
||||
g.yrange() default y axis range
|
||||
g.xlog() toggle x axis between linear and log
|
||||
g.ylog() toggle y axis between linear and log
|
||||
g.label(x,y,"text") place label at x,y coords
|
||||
g.curve(N,'r') set color of curve N
|
||||
|
||||
colors: 'k' = black, 'r' = red, 'g' = green, 'b' = blue
|
||||
'm' = magenta, 'c' = cyan, 'y' = yellow
|
||||
"""
|
||||
|
||||
# History
|
||||
# 8/05, Matt Jones (BYU): original version
|
||||
# 9/05, Steve Plimpton: added mplot() method
|
||||
|
||||
# ToDo list
|
||||
# allow choice of JPG or PNG or GIF when saving ?
|
||||
# can this be done from GnuPlot or have to do via ImageMagick convert ?
|
||||
# way to trim EPS plot that is created ?
|
||||
# hide does not work on Mac aqua
|
||||
# select does not pop window to front on Mac aqua
|
||||
|
||||
# Variables
|
||||
# current = index of current figure (1-N)
|
||||
# figures = list of figure objects with each plot's attributes
|
||||
# so they aren't lost between replots
|
||||
|
||||
# Imports and external programs
|
||||
|
||||
import os
|
||||
import sys
|
||||
|
||||
try: from DEFAULTS import PIZZA_GNUPLOT
|
||||
except ImportError: PIZZA_GNUPLOT = "gnuplot -p"
|
||||
try: from DEFAULTS import PIZZA_GNUTERM
|
||||
except ImportError: PIZZA_GNUTERM = "x11"
|
||||
|
||||
# Class definition
|
||||
|
||||
class gnu:
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def __init__(self):
|
||||
self.GNUPLOT = os.popen(PIZZA_GNUPLOT,'w')
|
||||
self.file = "tmp.gnu"
|
||||
self.figures = []
|
||||
self.select(1)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def stop(self):
|
||||
self.__call__("quit")
|
||||
del self.GNUPLOT
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def __call__(self,command):
|
||||
self.GNUPLOT.write(command + '\n')
|
||||
self.GNUPLOT.flush()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def enter(self):
|
||||
while 1:
|
||||
if sys.version_info[0] == 3:
|
||||
command = input("gnuplot> ")
|
||||
else:
|
||||
command = raw_input("gnuplot> ")
|
||||
if command == "quit" or command == "exit": return
|
||||
self.__call__(command)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# write plot vectors to files and plot them
|
||||
|
||||
def plot(self,*vectors):
|
||||
if len(vectors) == 1:
|
||||
file = self.file + ".%d.1" % self.current
|
||||
linear = range(len(vectors[0]))
|
||||
self.export(file,linear,vectors[0])
|
||||
self.figures[self.current-1].ncurves = 1
|
||||
else:
|
||||
if len(vectors) % 2: raise Exception("vectors must come in pairs")
|
||||
for i in range(0,len(vectors),2):
|
||||
file = self.file + ".%d.%d" % (self.current,i/2+1)
|
||||
self.export(file,vectors[i],vectors[i+1])
|
||||
self.figures[self.current-1].ncurves = len(vectors)/2
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# create multiple plots from growing vectors, save to numbered files
|
||||
# don't plot empty vector, create a [0] instead
|
||||
|
||||
def mplot(self,start,stop,skip,file,*vectors):
|
||||
n = 0
|
||||
for i in range(start,stop,skip):
|
||||
partial_vecs = []
|
||||
for vec in vectors:
|
||||
if i: partial_vecs.append(vec[:i])
|
||||
else: partial_vecs.append([0])
|
||||
self.plot(*partial_vecs)
|
||||
|
||||
if n < 10: newfile = file + "000" + str(n)
|
||||
elif n < 100: newfile = file + "00" + str(n)
|
||||
elif n < 1000: newfile = file + "0" + str(n)
|
||||
else: newfile = file + str(n)
|
||||
|
||||
self.save(newfile)
|
||||
n += 1
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# write list of equal-length vectors to filename
|
||||
|
||||
def export(self,filename,*vectors):
|
||||
n = len(vectors[0])
|
||||
for vector in vectors:
|
||||
if len(vector) != n: raise Exception("vectors must be same length")
|
||||
f = open(filename,'w')
|
||||
nvec = len(vectors)
|
||||
for i in range(n):
|
||||
for j in range(nvec):
|
||||
print(str(vectors[j][i])+" ",file=f,end='')
|
||||
print ("",file=f)
|
||||
f.close()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# select plot N as current plot
|
||||
|
||||
def select(self,n):
|
||||
self.current = n
|
||||
if len(self.figures) < n:
|
||||
for i in range(n - len(self.figures)):
|
||||
self.figures.append(figure())
|
||||
cmd = "set term " + PIZZA_GNUTERM + ' ' + str(n)
|
||||
self.__call__(cmd)
|
||||
if self.figures[n-1].ncurves: self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# delete window for plot N
|
||||
|
||||
def hide(self,n):
|
||||
cmd = "set term %s close %d" % (PIZZA_GNUTERM,n)
|
||||
self.__call__(cmd)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# save plot to file.eps
|
||||
# final re-select will reset terminal
|
||||
# do not continue until plot file is written out
|
||||
# else script could go forward and change data file
|
||||
# use tmp.done as semaphore to indicate plot is finished
|
||||
|
||||
def save(self,file):
|
||||
self.__call__("set terminal postscript enhanced solid lw 2 color portrait")
|
||||
cmd = "set output '%s.eps'" % file
|
||||
self.__call__(cmd)
|
||||
if os.path.exists("tmp.done"): os.remove("tmp.done")
|
||||
self.draw()
|
||||
self.__call__("!touch tmp.done")
|
||||
while not os.path.exists("tmp.done"): continue
|
||||
self.__call__("set output")
|
||||
self.select(self.current)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# restore default attributes by creating a new fig object
|
||||
|
||||
def erase(self):
|
||||
fig = figure()
|
||||
fig.ncurves = self.figures[self.current-1].ncurves
|
||||
self.figures[self.current-1] = fig
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def aspect(self,value):
|
||||
self.figures[self.current-1].aspect = value
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def xrange(self,*values):
|
||||
if len(values) == 0:
|
||||
self.figures[self.current-1].xlimit = 0
|
||||
else:
|
||||
self.figures[self.current-1].xlimit = (values[0],values[1])
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def yrange(self,*values):
|
||||
if len(values) == 0:
|
||||
self.figures[self.current-1].ylimit = 0
|
||||
else:
|
||||
self.figures[self.current-1].ylimit = (values[0],values[1])
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def label(self,x,y,text):
|
||||
self.figures[self.current-1].labels.append((x,y,text))
|
||||
self.figures[self.current-1].nlabels += 1
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def nolabels(self):
|
||||
self.figures[self.current-1].nlabel = 0
|
||||
self.figures[self.current-1].labels = []
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def title(self,*strings):
|
||||
if len(strings) == 1:
|
||||
self.figures[self.current-1].title = strings[0]
|
||||
else:
|
||||
self.figures[self.current-1].title = strings[0]
|
||||
self.figures[self.current-1].xtitle = strings[1]
|
||||
self.figures[self.current-1].ytitle = strings[2]
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def xtitle(self,label):
|
||||
self.figures[self.current-1].xtitle = label
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def ytitle(self,label):
|
||||
self.figures[self.current-1].ytitle = label
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def xlog(self):
|
||||
if self.figures[self.current-1].xlog:
|
||||
self.figures[self.current-1].xlog = 0
|
||||
else:
|
||||
self.figures[self.current-1].xlog = 1
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def ylog(self):
|
||||
if self.figures[self.current-1].ylog:
|
||||
self.figures[self.current-1].ylog = 0
|
||||
else:
|
||||
self.figures[self.current-1].ylog = 1
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def curve(self,num,color):
|
||||
fig = self.figures[self.current-1]
|
||||
while len(fig.colors) < num: fig.colors.append(0)
|
||||
fig.colors[num-1] = colormap[color]
|
||||
self.draw()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# draw a plot with all its settings
|
||||
# just return if no files of vectors defined yet
|
||||
|
||||
def draw(self):
|
||||
fig = self.figures[self.current-1]
|
||||
if not fig.ncurves: return
|
||||
|
||||
cmd = 'set size ratio ' + str(1.0/float(fig.aspect))
|
||||
self.__call__(cmd)
|
||||
|
||||
cmd = 'set title ' + '"' + fig.title + '"'
|
||||
self.__call__(cmd)
|
||||
cmd = 'set xlabel ' + '"' + fig.xtitle + '"'
|
||||
self.__call__(cmd)
|
||||
cmd = 'set ylabel ' + '"' + fig.ytitle + '"'
|
||||
self.__call__(cmd)
|
||||
|
||||
if fig.xlog: self.__call__("set logscale x")
|
||||
else: self.__call__("unset logscale x")
|
||||
if fig.ylog: self.__call__("set logscale y")
|
||||
else: self.__call__("unset logscale y")
|
||||
if fig.xlimit:
|
||||
cmd = 'set xr [' + str(fig.xlimit[0]) + ':' + str(fig.xlimit[1]) + ']'
|
||||
self.__call__(cmd)
|
||||
else: self.__call__("set xr [*:*]")
|
||||
if fig.ylimit:
|
||||
cmd = 'set yr [' + str(fig.ylimit[0]) + ':' + str(fig.ylimit[1]) + ']'
|
||||
self.__call__(cmd)
|
||||
else: self.__call__("set yr [*:*]")
|
||||
|
||||
self.__call__("set nolabel")
|
||||
for i in range(fig.nlabels):
|
||||
x = fig.labels[i][0]
|
||||
y = fig.labels[i][1]
|
||||
text = fig.labels[i][2]
|
||||
cmd = 'set label ' + '\"' + text + '\" at ' + str(x) + ',' + str(y)
|
||||
self.__call__(cmd)
|
||||
|
||||
self.__call__("set key off")
|
||||
cmd = 'plot '
|
||||
for i in range(int(fig.ncurves)):
|
||||
file = self.file + ".%d.%d" % (self.current,i+1)
|
||||
if len(fig.colors) > i and fig.colors[i]:
|
||||
cmd += "'" + file + "' using 1:2 with line %d, " % fig.colors[i]
|
||||
else:
|
||||
cmd += "'" + file + "' using 1:2 with lines, "
|
||||
self.__call__(cmd[:-2])
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# class to store settings for a single plot
|
||||
|
||||
class figure:
|
||||
|
||||
def __init__(self):
|
||||
self.ncurves = 0
|
||||
self.colors = []
|
||||
self.title = ""
|
||||
self.xtitle = ""
|
||||
self.ytitle = ""
|
||||
self.aspect = 1.3
|
||||
self.xlimit = 0
|
||||
self.ylimit = 0
|
||||
self.xlog = 0
|
||||
self.ylog = 0
|
||||
self.nlabels = 0
|
||||
self.labels = []
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# line color settings
|
||||
|
||||
colormap = {'k':-1, 'r':1, 'g':2, 'b':3, 'm':4, 'c':5, 'y':7}
|
||||
1
python/examples/pizza/gnu.py
Symbolic link
1
python/examples/pizza/gnu.py
Symbolic link
@ -0,0 +1 @@
|
||||
../../../tools/python/pizza/gnu.py
|
||||
@ -1,299 +0,0 @@
|
||||
# Pizza.py toolkit, https://lammps.github.io/pizza
|
||||
# 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.
|
||||
|
||||
# for python3 compatibility
|
||||
from __future__ import print_function
|
||||
|
||||
# pdb tool
|
||||
|
||||
oneline = "Read, write PDB files in combo with LAMMPS snapshots"
|
||||
|
||||
docstr = """
|
||||
p = pdbfile("3CRO") create pdb object from PDB file or WWW
|
||||
p = pdbfile("pep1 pep2") read in multiple PDB files
|
||||
p = pdbfile("pep*") can use wildcards
|
||||
p = pdbfile(d) read in snapshot data with no PDB file
|
||||
p = pdbfile("3CRO",d) read in single PDB file with snapshot data
|
||||
|
||||
string arg contains one or more PDB files
|
||||
don't need .pdb suffix except wildcard must expand to file.pdb
|
||||
if only one 4-char file specified and it is not found,
|
||||
it will be downloaded from http://www.rcsb.org as 3CRO.pdb
|
||||
d arg is object with atom coordinates (dump, data)
|
||||
|
||||
p.one() write all output as one big PDB file to tmp.pdb
|
||||
p.one("mine") write to mine.pdb
|
||||
p.many() write one PDB file per snapshot: tmp0000.pdb, ...
|
||||
p.many("mine") write as mine0000.pdb, mine0001.pdb, ...
|
||||
p.single(N) write timestamp N as tmp.pdb
|
||||
p.single(N,"new") write as new.pdb
|
||||
|
||||
how new PDB files are created depends on constructor inputs:
|
||||
if no d: one new PDB file for each file in string arg (just a copy)
|
||||
if only d specified: one new PDB file per snapshot in generic format
|
||||
if one file in str arg and d: one new PDB file per snapshot
|
||||
using input PDB file as template
|
||||
multiple input PDB files with a d is not allowed
|
||||
|
||||
index,time,flag = p.iterator(0)
|
||||
index,time,flag = p.iterator(1)
|
||||
|
||||
iterator = loop over number of PDB files
|
||||
call first time with arg = 0, thereafter with arg = 1
|
||||
N = length = # of snapshots or # of input PDB files
|
||||
index = index of snapshot or input PDB file (0 to N-1)
|
||||
time = timestep value (time stamp for snapshot, index for multiple PDB)
|
||||
flag = -1 when iteration is done, 1 otherwise
|
||||
typically call p.single(time) in iterated loop to write out one PDB file
|
||||
"""
|
||||
|
||||
# History
|
||||
# 8/05, Steve Plimpton (SNL): original version
|
||||
# 3/17, Richard Berger (Temple U): improve Python 3 compatibility
|
||||
|
||||
# ToDo list
|
||||
# for generic PDB file (no template) from a LJ unit system,
|
||||
# the atoms in PDB file are too close together
|
||||
|
||||
# Variables
|
||||
# files = list of input PDB files
|
||||
# data = data object (ccell,data,dump) to read snapshots from
|
||||
# atomlines = dict of ATOM lines in original PDB file
|
||||
# key = atom id, value = tuple of (beginning,end) of line
|
||||
|
||||
# Imports and external programs
|
||||
|
||||
import sys, glob, urllib
|
||||
PY3 = sys.version_info[0] == 3
|
||||
|
||||
if PY3:
|
||||
string_types = str,
|
||||
else:
|
||||
string_types = basestring
|
||||
|
||||
# Class definition
|
||||
|
||||
class pdbfile:
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def __init__(self,*args):
|
||||
if len(args) == 1:
|
||||
if type(args[0]) is string_types:
|
||||
filestr = args[0]
|
||||
self.data = None
|
||||
else:
|
||||
filestr = None
|
||||
self.data = args[0]
|
||||
elif len(args) == 2:
|
||||
filestr = args[0]
|
||||
self.data = args[1]
|
||||
else: raise Exception("invalid args for pdb()")
|
||||
|
||||
# flist = full list of all PDB input file names
|
||||
# append .pdb if needed
|
||||
|
||||
if filestr:
|
||||
list = filestr.split()
|
||||
flist = []
|
||||
for file in list:
|
||||
if '*' in file: flist += glob.glob(file)
|
||||
else: flist.append(file)
|
||||
for i in range(len(flist)):
|
||||
if flist[i][-4:] != ".pdb": flist[i] += ".pdb"
|
||||
if len(flist) == 0:
|
||||
raise Exception("no PDB file specified")
|
||||
self.files = flist
|
||||
else: self.files = []
|
||||
|
||||
if len(self.files) > 1 and self.data:
|
||||
raise Exception("cannot use multiple PDB files with data object")
|
||||
if len(self.files) == 0 and not self.data:
|
||||
raise Exception("no input PDB file(s)")
|
||||
|
||||
# grab PDB file from http://rcsb.org if not a local file
|
||||
|
||||
if len(self.files) == 1 and len(self.files[0]) == 8:
|
||||
try:
|
||||
open(self.files[0],'r').close()
|
||||
except:
|
||||
print("downloading %s from http://rcsb.org" % self.files[0])
|
||||
fetchstr = "http://www.rcsb.org/pdb/cgi/export.cgi/%s?format=PDB&pdbId=2cpk&compression=None" % self.files[0]
|
||||
urllib.urlretrieve(fetchstr,self.files[0])
|
||||
|
||||
if self.data and len(self.files): self.read_template(self.files[0])
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# write a single large PDB file for concatenating all input data or files
|
||||
# if data exists:
|
||||
# only selected atoms returned by extract
|
||||
# atoms written in order they appear in snapshot
|
||||
# atom only written if its tag is in PDB template file
|
||||
# if no data:
|
||||
# concatenate all input files to one output file
|
||||
|
||||
def one(self,*args):
|
||||
if len(args) == 0: file = "tmp.pdb"
|
||||
elif args[0][-4:] == ".pdb": file = args[0]
|
||||
else: file = args[0] + ".pdb"
|
||||
|
||||
f = open(file,'w')
|
||||
|
||||
# use template PDB file with each snapshot
|
||||
|
||||
if self.data:
|
||||
n = flag = 0
|
||||
while 1:
|
||||
which,time,flag = self.data.iterator(flag)
|
||||
if flag == -1: break
|
||||
self.convert(f,which)
|
||||
print("END",file=f)
|
||||
print(time,end='')
|
||||
sys.stdout.flush()
|
||||
n += 1
|
||||
|
||||
else:
|
||||
for file in self.files:
|
||||
f.write(open(file,'r').read())
|
||||
print("END",file=f)
|
||||
print(file,end='')
|
||||
sys.stdout.flush()
|
||||
|
||||
f.close()
|
||||
print("\nwrote %d datasets to %s in PDB format" % (n,file))
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# write series of numbered PDB files
|
||||
# if data exists:
|
||||
# only selected atoms returned by extract
|
||||
# atoms written in order they appear in snapshot
|
||||
# atom only written if its tag is in PDB template file
|
||||
# if no data:
|
||||
# just copy all input files to output files
|
||||
|
||||
def many(self,*args):
|
||||
if len(args) == 0: root = "tmp"
|
||||
else: root = args[0]
|
||||
|
||||
if self.data:
|
||||
n = flag = 0
|
||||
while 1:
|
||||
which,time,flag = self.data.iterator(flag)
|
||||
if flag == -1: break
|
||||
|
||||
if n < 10:
|
||||
file = root + "000" + str(n)
|
||||
elif n < 100:
|
||||
file = root + "00" + str(n)
|
||||
elif n < 1000:
|
||||
file = root + "0" + str(n)
|
||||
else:
|
||||
file = root + str(n)
|
||||
file += ".pdb"
|
||||
|
||||
f = open(file,'w')
|
||||
self.convert(f,which)
|
||||
f.close()
|
||||
|
||||
print(time,end='')
|
||||
sys.stdout.flush()
|
||||
n += 1
|
||||
|
||||
else:
|
||||
n = 0
|
||||
for infile in self.files:
|
||||
if n < 10:
|
||||
file = root + "000" + str(n)
|
||||
elif n < 100:
|
||||
file = root + "00" + str(n)
|
||||
elif n < 1000:
|
||||
file = root + "0" + str(n)
|
||||
else:
|
||||
file = root + str(n)
|
||||
file += ".pdb"
|
||||
|
||||
f = open(file,'w')
|
||||
f.write(open(infile,'r').read())
|
||||
f.close()
|
||||
print(file,end='')
|
||||
sys.stdout.flush()
|
||||
|
||||
n += 1
|
||||
|
||||
print("\nwrote %d datasets to %s*.pdb in PDB format" % (n,root))
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# write a single PDB file
|
||||
# if data exists:
|
||||
# time is timestamp in snapshot
|
||||
# only selected atoms returned by extract
|
||||
# atoms written in order they appear in snapshot
|
||||
# atom only written if its tag is in PDB template file
|
||||
# if no data:
|
||||
# time is index into list of input PDB files
|
||||
# just copy one input file to output file
|
||||
|
||||
def single(self,time,*args):
|
||||
if len(args) == 0: file = "tmp.pdb"
|
||||
elif args[0][-4:] == ".pdb": file = args[0]
|
||||
else: file = args[0] + ".pdb"
|
||||
f = open(file,'w')
|
||||
|
||||
if self.data:
|
||||
which = self.data.findtime(time)
|
||||
self.convert(f,which)
|
||||
else:
|
||||
f.write(open(self.files[time],'r').read())
|
||||
|
||||
f.close()
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# iterate over list of input files or selected snapshots
|
||||
# latter is done via data objects iterator
|
||||
|
||||
def iterator(self,flag):
|
||||
if not self.data:
|
||||
if not flag: self.iterate = 0
|
||||
else:
|
||||
self.iterate += 1
|
||||
if self.iterate > len(self.files): return 0,0,-1
|
||||
return self.iterate,self.iterate,1
|
||||
|
||||
return self.data.iterator(flag)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# read a PDB file and store ATOM lines
|
||||
|
||||
def read_template(self,file):
|
||||
lines = open(file,'r').readlines()
|
||||
self.atomlines = {}
|
||||
for line in lines:
|
||||
if line.find("ATOM") == 0:
|
||||
tag = int(line[4:11])
|
||||
begin = line[:30]
|
||||
end = line[54:]
|
||||
self.atomlines[tag] = (begin,end)
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# convert one set of atoms to PDB format and write to f
|
||||
|
||||
def convert(self,f,which):
|
||||
time,box,atoms,bonds,tris,lines = self.data.viz(which)
|
||||
if len(self.files):
|
||||
for atom in atoms:
|
||||
id = atom[0]
|
||||
if self.atomlines.has_key(id):
|
||||
(begin,end) = self.atomlines[id]
|
||||
line = "%s%8.3f%8.3f%8.3f%s" % (begin,atom[2],atom[3],atom[4],end)
|
||||
print(line,file=f,end='')
|
||||
else:
|
||||
for atom in atoms:
|
||||
begin = "ATOM %6d %2d R00 1 " % (atom[0],atom[1])
|
||||
middle = "%8.3f%8.3f%8.3f" % (atom[2],atom[3],atom[4])
|
||||
end = " 1.00 0.00 NONE"
|
||||
print(begin+middle+end,file=f)
|
||||
1
python/examples/pizza/pdbfile.py
Symbolic link
1
python/examples/pizza/pdbfile.py
Symbolic link
@ -0,0 +1 @@
|
||||
../../../tools/python/pizza/pdbfile.py
|
||||
@ -300,7 +300,7 @@ class ElemwiseModels(torch.nn.Module):
|
||||
self.subnets = subnets
|
||||
self.n_types = n_types
|
||||
|
||||
def forward(self, descriptors, elems):
|
||||
def forward(self, descriptors, elems, dtype=torch.float64):
|
||||
"""
|
||||
Feeds descriptors to network model after adding zeros into
|
||||
descriptor columns relating to different atom types
|
||||
@ -319,8 +319,12 @@ class ElemwiseModels(torch.nn.Module):
|
||||
Per atom attribute computed by the network model
|
||||
"""
|
||||
|
||||
per_atom_attributes = torch.zeros(elems.size[0])
|
||||
self.dtype=dtype
|
||||
self.to(self.dtype)
|
||||
|
||||
per_atom_attributes = torch.zeros(elems.size(dim=0), dtype=self.dtype)
|
||||
given_elems, elem_indices = torch.unique(elems, return_inverse=True)
|
||||
for i, elem in enumerate(given_elems):
|
||||
per_atom_attribute[elem_indices == i] = self.subnets[elem](descriptors[elem_indices == i])
|
||||
self.subnets[elem].to(self.dtype)
|
||||
per_atom_attributes[elem_indices == i] = self.subnets[elem](descriptors[elem_indices == i]).flatten()
|
||||
return per_atom_attributes
|
||||
|
||||
Reference in New Issue
Block a user