def read_all_bodyfiles(prefix):
filenames = ff.find_sorted_local_input_fileset(prefix)
# Ignore log files
for i in range(len(filenames)):
if '.log' in filenames[i]:
print('Removing log file ', filenames[i])
filenames.remove(filenames[i])
nbodies = len(filenames)
print('Reading data for ', nbodies, ' bodies')
data = []
for i in range(nbodies):
filename = filenames[i]
print('Reading ', filename)
data.append(read_body_file(filename))
return filenames, data
def obtain_planet_tracks(prefix):
'''Reads all planetary data and creates tracks for each planet'''
planetfiles = ff.find_sorted_local_input_fileset(prefix + "*planets*")
time, nplanet, nactive, active, mp, ap, tmig = read_planets(planetfiles[1])
time_all = np.zeros(len(planetfiles) - 1)
active_all = np.zeros((nplanet, len(planetfiles) - 1))
ap_all = np.zeros((nplanet, len(planetfiles) - 1))
mp_all = np.zeros((nplanet, len(planetfiles) - 1))
tmig_all = np.zeros((nplanet, len(planetfiles) - 1))
for i in range(len(planetfiles) - 1):
time_all[i], nplanet, nactive, active, mp, ap, tmig = read_planets(
planetfiles[i + 1], verbose=False)
active_all[:, i] = active[:]
mp_all[:, i] = mp[:]
ap_all[:, i] = ap[:]
tmig_all[:, i] = tmig[:]
return time_all, nplanet, active_all, ap_all, mp_all, tmig_all
import filefinder as ff
from os import system
# Get list of all directories
paramfilelist = ff.find_sorted_local_input_fileset("*.params")
nfiles = len(paramfilelist)
print "There are ", nfiles, " files"
# for blocks of 500, create a folder and move them
ifile = 0
inext = 0
current_dir = ""
for ifile in range(nfiles):
if ifile == inext:
inext = inext + 500
current_dir = "run_to_" + str(inext)
# Create new directory
command = "mkdir " + current_dir
print command
system(command)
# Copy essential executable files
command = "cp job-placeholder " + current_dir
import filefinder as ff
from numpy import genfromtxt
from os import system
# Get list of all directories
directorylist = genfromtxt('directorylist', dtype='string')
print directorylist
for directory in directorylist:
# Get list of all job script files in directory
jobfilelist = ff.find_sorted_local_input_fileset(directory + "/job_*")
nfiles = len(jobfilelist)
print "There are ", nfiles, " files"
# Submit each job using sbatch
for jobfile in jobfilelist:
command = "sbatch " + jobfile
print command
system(command)
# Written 26/1/17 by dh4gan
# Takes outputs from multiple runs of the grapus model and stitches them together
# Primarily, this is ensuring that the 'istar' variable is corrected
import numpy as np
import filefinder as ff
from sys import exit
from io_grapus import ninitialcol,nlogcol,nfinalcol,logcoldict,finalcoldict, initialfmt,finalfmt,logfmt
# Find three (sorted) file lists containing all initial, final and log files to be built
initialfiles = ff.find_sorted_local_input_fileset('*.initial')
finalfiles = ff.find_sorted_local_input_fileset('*.final')
logfiles = ff.find_sorted_local_input_fileset('*.log')
ninitial = len(initialfiles)
nfinal = len(finalfiles)
nlog = len(logfiles)
if ninitial!=nfinal or nfinal!=nlog:
print 'Unequal file counts: '
print 'Initial files ',ninitial
print 'Final files ',nfinal
print 'Log files ',nlog
exit()
# Define the total file names
totalinitialfile = 'total.initial'
totalfinalfile = 'total.final'
import filefinder as ff
from os import system
# Get list of all job script files in directory
jobfilelist = ff.find_sorted_local_input_fileset("job_*")
nfiles = len(jobfilelist)
print "There are ", nfiles, " files"
# Submit each job using sbatch
#for jobfile in jobfilelist:
nmin = 51
nmax = 100
for i in range(nmax):
jobfile = jobfilelist[i]
command = "sbatch "+jobfile
print command
system(command)
def plot_profile_multifiles_variable(prefix, add_planets=False):
'''Reads multiple profile files and plots a specific variable'''
filenames = ff.find_sorted_local_input_fileset(prefix + "*profile*")
nfiles = len(filenames)
initial = input('Starting filenumber? ')
final = input('Final filenumber? ')
print 'Now select variable to plot: here are the choices'
for i in range(len(profilekeys)):
print str(i + 1) + ': ' + profilekeys[i]
var = input('Which variable (1-' + str(len(profilekeys)) + ')? ')
var = var - 1
if (final > nfiles):
print "Limiting count to available files"
final = nfiles
fig1 = plt.figure()
ax = fig1.add_subplot(111)
if (add_planets):
planetfiles = ff.find_sorted_local_input_fileset(prefix + "*planets*")
initial = initial - 1
final = final - 1
for i in range(initial, final):
time, profdata = read_profile(filenames[i])
if (add_planets):
t, nplanet, nactive, active, mp, ap, tmig = read_planets(
planetfiles[i], verbose=False)
# Setup planet points for plotting
xpoints = np.zeros(nplanet)
ypoints = np.zeros(nplanet)
if profileymin[var] != profileymax[var]:
ypoints[:] = 2.0 * profileymin[var]
else:
ypoints[:] = 2.0 * np.min(profdata[:, var])
planetsizes, planetcolours = get_planet_size_and_colour(
nplanet, mp)
if (profileylog[var]):
ax.set_xscale('log')
ax.set_yscale('log')
if (profileymin[var] != profileymax[var]):
ax.set_ylim(profileymin[var], profileymax[var])
line1 = ax.plot(profdata[:, 0], profdata[:, var])
ax.set_xlabel(profilexlabel)
ax.set_ylabel(profilelabels[var])
ax.text(0.9,
0.9,
't = ' + str(np.round(time, 2)) + ' yr',
bbox=dict(edgecolor='black', facecolor='none'),
horizontalalignment='center',
verticalalignment='center',
transform=ax.transAxes)
if (add_planets):
ax.scatter(ap, ypoints, s=planetsizes, facecolor=planetcolours)
outputfile = profilekeys[var] + '_' + filenames[i] + '.png'
print 'Saving to ', outputfile
plt.savefig(outputfile, format='png')
ax.clear()
