def parseAndRun(executable, configFile, runDir, args=None):
# Build run dir name
print "Parsing configuration...\nConfigFile: " + configFile + "\nRunDir: " + runDir
configFileDir, configFileName = split(configFile)
if runDir == "":
runDir = join(configFileDir, "runs", dateDir)
makedirsSilent(runDir)
config = Config()
config.readFile(configFile)
if config.exists("runConfig.subConfigs"):
print "This is a parallel config. Launching subconfigs..."
for subConfigValue in config.children("runConfig.subConfigs"):
subConfigFile = join(configFileDir, config.value(subConfigValue)[0])
subConfigFileDir, subConfigFileName = split(subConfigFile)
subConfigRunDir = join(runDir, subConfigFileName).replace(".cfg", "")
parseAndRun(executable, subConfigFile, subConfigRunDir, args)
config.writeFile(join(runDir, configFileName))
else:
print "This is a singular config. Launching it alone..."
runConfigFile = join(runDir, configFileName)
config.writeFile(runConfigFile)
run(executable, runConfigFile, dateDir, runDir, args)
def selectConfig(configFilePath):
if isdir(configFilePath):
foundConfig = False
for fileName in listdir(configFilePath):
if fileName[-4:] == ".cfg":
configFilePath = join(configFilePath, fileName)
foundConfig = True
break
if not foundConfig:
print "Could not find config..."
raise FileIOException
print "Loading config " + configFilePath + "\n"
configFilePath = abspath(configFilePath)
config = Config()
config.readFile(configFilePath)
symlinkNameConfig = "/tmp/latestconfig.cfg"
print "Target: " + configFilePath
print "Name: " + symlinkNameConfig
createSymlink(configFilePath, symlinkNameConfig)
saveFilePath, saveFileName = split(config.value("simulation.saveFileName")[0])
saveFilePath = expanduser(saveFilePath)
symLinkNameSave = "/tmp/latestsavedir"
print "Target: " + saveFilePath
print "Name: " + symLinkNameSave
createSymlink(saveFilePath, symLinkNameSave)
#from runconfig import run
from pylibconfig import Config
from pylab import *
from sys import argv
from os.path import split, join
from fys4460 import makedirsSilent
defaultConfigFilePath = "1-equilibrated-fast-zoom/default-start.cfg"
defaultEndConfigFilePath = "1-equilibrated-fast-zoom/default-end.cfg"
defaultConfigDir, defaultConfigFileName = split(defaultConfigFilePath)
defaultEndConfigDir, defaultEndConfigFileName = split(defaultEndConfigFilePath)
temperatures = linspace(100, 600, 40)
config = Config()
config.addGroup("", "runConfig")
config.addList("runConfig", "subConfigs")
iRun = 0
for temperature in temperatures:
runName = "temperature%04d" % iRun
subConfigFileName = join(runName, "step0.cfg")
subConfigEndFileName = join(runName, "step1.cfg")
subConfigFilePath = join(defaultConfigDir, subConfigFileName)
subConfigEndFilePath = join(defaultConfigDir, subConfigEndFileName)
makedirsSilent(split(subConfigFilePath)[0])
subConfigStart = Config()
subConfigStart.readFile(defaultConfigFilePath)
oldSaveFile = subConfigStart.value("simulation.saveFileName")[0]
newSaveFile = oldSaveFile.replace("$DATEDIR", "$DATEDIR/" + runName)
#!/usr/bin/env python
import sys
if len(sys.argv) != 2:
raise SystemExit("Provide a path to the config file you wish to read")
from pylibconfig import Config
config = Config()
try:
config.readFile(sys.argv[1])
print "Config loaded"
sys.exit(0)
except Exception as e:
print "Config failed to read :("
print e
sys.exit(1)
from fys4460 import loadAtoms
from glob import glob
runDir = argv[1]
saveDir = split(argv[1])[0]
temperatureDirs = listdir(runDir)
temperatureDirs.sort()
saveFileNamesList = []
nFilenames = 0
for temperatureDir in temperatureDirs:
if not isdir(join(runDir, temperatureDir)):
continue
print "Loading dir " + temperatureDir
config = Config()
configFileName = join(runDir, temperatureDir, "step1", "step1.cfg")
print "Loading config " + configFileName
config.readFile(configFileName)
saveFileNames = config.value("simulation.saveFileName")[0]
saveFileNames = expanduser(saveFileNames)
saveFileNames = glob(saveFileNames)
saveFileNames.sort()
saveFileNamesSelection = saveFileNames[300:399]
saveFileNamesList.append(saveFileNamesSelection)
nFilenames += len(saveFileNamesSelection)
pressures = zeros(nFilenames)
temperatures = zeros(nFilenames)
pressuresAverage = zeros(len(saveFileNamesList))
@author: svenni
"""
#from runconfig import run
from pylibconfig import Config
from pylab import *
from sys import argv
from os.path import split, join
from fys4460 import makedirsSilent
defaultConfigFilePath = "1k-temperature/default.cfg"
defaultConfigDir, defaultConfigFileName = split(defaultConfigFilePath)
systemSizes = [6, 7, 8, 9, 10, 11, 12]
config = Config()
config.addGroup("", "runConfig")
config.addList("runConfig", "subConfigs")
iRun = 0
for systemSize in systemSizes:
runName = "systemsize%04d" % systemSize
subConfigFileName = join(runName, runName + ".cfg")
subConfigFilePath = join(defaultConfigDir, subConfigFileName)
print split(subConfigFilePath)[0]
makedirsSilent(split(subConfigFilePath)[0])
subConfig = Config()
subConfig.readFile(defaultConfigFilePath)
subConfig.setValue("initialization.[0].nCells", systemSize)
saveFileName = subConfig.value("simulation.saveFileName")[0]
saveFileName = saveFileName.replace("$DATEDIR", "$DATEDIR/" + runName)
def test_greeting(self):
config = Config()
config.addString("", "test")
config.addBool("test_bool", True)
config.setValue("test", "value")
self.assert_(config.value("test")[0] == "value")
self.assert_(config.value("test")[1] == True)
self.assert_(config.value("loose")[1] == False)
self.assert_(config.value("test_bool")[0] == True)
config.setValue("test_bool", False)
config.writeFile("test.conf")
self.assert_(os.path.exists("./test.conf") == True)
config.readFile("test.conf")
self.assert_(config.value("test")[0] == "value")
self.assert_(config.value("test")[1] == True)
os.remove("./test.conf")
def test_greeting ( self ):
config = Config ()
config.addString ( "", "test" )
config.setValue ( "test", "value" )
config.addBoolean ( "", "test_bool")
config.setValue ( "test_bool", True )
config.addInteger ( "", "test_int")
config.setValue ( "test_int", 9 )
config.addInteger ( "", "test_unsigned_int")
config.setValue ( "test_unsigned_int", -9 )
config.addFloat ( "", "test_float")
config.setValue ( "test_float", 82.1002 )
self.assert_ ( config.value ( "test" )[0] == "value" )
self.assert_ ( config.value ( "test" )[1] == True )
self.assert_ ( config.value ( "test_bool" )[0] == True )
self.assert_ ( config.value ( "loose" )[1] == False )
self.assert_ ( config.value ( "test_int" )[0] == 9 )
self.assert_ ( config.value ( "test_unsigned_int" )[0] == -9 )
self.assert_ ( fabs( config.value ( "test_float" )[0] - 82.1002) < 0.00001 )
config.setValue( "test_bool", False )
config.writeFile ( "test.conf" )
self.assert_ ( os.path.exists ( "./test.conf" ) == True )
config.readFile ( "test.conf" )
self.assert_ ( config.value ( "test" )[0] == "value" )
self.assert_ ( config.value ( "test" )[1] == True )
os.remove ( "./test.conf" )
def test_greeting(self):
config = Config()
config.addString("", "test")
config.setValue("test", "value")
config.addBoolean("", "test_bool")
config.setValue("test_bool", True)
config.addInteger("", "test_int")
config.setValue("test_int", 9)
config.addInteger("", "test_unsigned_int")
config.setValue("test_unsigned_int", -9)
config.addFloat("", "test_float")
config.setValue("test_float", 82.1002)
self.assert_(config.value("test")[0] == "value")
self.assert_(config.value("test")[1] == True)
self.assert_(config.value("test_bool")[0] == True)
self.assert_(config.value("loose")[1] == False)
self.assert_(config.value("test_int")[0] == 9)
self.assert_(config.value("test_unsigned_int")[0] == -9)
self.assert_(fabs(config.value("test_float")[0] - 82.1002) < 0.00001)
config.setValue("test_bool", False)
config.writeFile("test.conf")
self.assert_(os.path.exists("./test.conf") == True)
config.readFile("test.conf")
self.assert_(config.value("test")[0] == "value")
self.assert_(config.value("test")[1] == True)
os.remove("./test.conf")
"""
path = "/home/henrik/NumericalData/FYS4460/2048_diffusion3/"
names = ["mdsim0002", "mdsim0005"]#, "mdsim0008"]#, "mdsim0011", "mdsim0014", "mdsim0017", "mdsim0020", "mdsim0023"]#, "mdsim0005"]
"""
# Long diffusion run
path = "/home/henrik/NumericalData/FYS4460/2048_diffusion_long6/"
names = ["mdsim0002", "mdsim0005"]
fig1 = plt.figure(); fig1ax = plt.axes(); fig2 = plt.figure(); fig2ax = plt.axes();
legendstring = [];
for name in names:
infileVMD = open(path+name+"/out.xyz")
infileData = open(path+name+"/measures.dat")
config = Config()
config.readFile(path+name+"/"+name+".cfg")
temperature = config.value("system.temperature")[0]
num_particles = int(infileVMD.readline());
print "Num particles = ", num_particles
measures = infileData.readlines()
vmd = infileVMD.readlines();
vmd = vmd[1:-1]
n_t = int(len(measures)-1);
t = np.zeros(n_t)
for i in range(n_t):
tmp = measures[i+1].split()
t[i] = float(tmp[0]);
print "Num timesteps = ", n_t
particle_square_displacements = np.zeros((num_particles, n_t))
particle_initial_positions = np.zeros((num_particles, 3));
#!/usr/bin/env python
import sys
if len(sys.argv) != 2:
raise SystemExit("Provide a path to the config file you wish to read")
from pylibconfig import Config
config = Config ()
try:
config.readFile ( sys.argv[1] )
print "Config loaded"
sys.exit(0)
except Exception as e:
print "Config failed to read :("
print e
sys.exit(1)
def run(executable, configFile, dateDir, runDir, args=None):
executable = os.path.realpath(executable)
temp,configFileName = os.path.split(configFile)
configName = configFileName.replace(".cfg", "")
config = Config()
config.readFile(configFile)
replaceDateDir(config, dateDir)
if(config.exists("runInformation")):
if args.force:
config.remove("", "runInformation")
else:
print "Config cannot contain section runInformation already. It would be overwritten."
raise Exception
### Git info ###
# repo = Repo(".")
# head = repo.heads[0]
# commitSHA = getattr(head.commit, "id")
commitSHA = "N/A"
### Run information ###
config.addGroup("", "runInformation")
addRunInformation(config, "hostname", socket.gethostname())
addRunInformation(config, "timestamp", datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
addRunInformation(config, "gitCommitSHA", commitSHA)
addRunInformation(config, "dateDir", dateDir)
addRunInformation(config, "runDir", runDir)
addRunInformation(config, "configFile", configFile)
config.writeFile(configFile)
selectConfig(os.path.abspath(configFile))
# Input stuff to database
# database = sqlite3.connect("test.db")
# values = [executable, runDir]
# insertID = database.execute("INSERT INTO run (executable, dir) VALUES (?, ?)", values)
# printChildren(database, insertID.lastrowid, config, "")
# database.commit()
# database.close()
# Create symlinks
# createSymlink(os.getcwd() + "/" + runDir, "/tmp/latest")
# saveFile = config.value("simulation.saveFileName")[0]
# saveFile = expanduser(saveFile)
# saveDir = os.path.dirname(saveFile)
# createSymlink(saveDir, "/tmp/latestsavedir")
runList = []
nProcesses = 1
if config.exists("mpi"):
nProcesses = config.value("mpi.nProcesses")[0]
runList = ["mpirun", "-n", str(nProcesses), "nice", "-n", "19", executable, configFileName]
else:
runList = ["nice", "-n", "19", executable, configFileName]
logFilePath = join(runDir, "run_" + configFileName.replace(".cfg", "") + ".log")
f = open(logFilePath, "w")
print "RunList: " + str(runList) + "\nRunDir: " + runDir + "\nLogFile: " + logFilePath
print "Starting..."
# try:
# progressProcessList = ["python", "progressreporter.py", configName + " " + runDir, join(runDir, "runprogress.txt")]
# progressProcess = subprocess.Popen(progressProcessList)
process = subprocess.Popen(runList, cwd=runDir, stdout=f, stderr=subprocess.STDOUT)
process.wait()
# print "Waiting for progressreporter to finish..."
# progressProcess.wait()
# except Exception:
# process.kill()
# f.close()
f.close()
self.config.setValue("settings.sim_name", "mdsim%.4d" % self.counter)
self.config.setValue("settings.output_path", self.path + self.config.value("settings.sim_name")[0] + "/");
os.makedirs(self.config.value("settings.output_path")[0]);
self.config.writeFile(self.config.value("settings.output_path")[0] +"mdsim%.4d.cfg" % self.counter)
self.counter += 1;
def set_potential(self, p = 'lennard_jones'):
if p == 'lennard_jones':
self.config.setValue("system.potential", 0)
else:
print "No support for potential different from Lennard jones ('lennard_jones')"
inPath = "/home/henrik/Dropbox/Henrik/Emner/FYS4460/project1/config/"
outPath = "/home/henrik/NumericalData/FYS4460/2048_diffusion_long6/"
config = Config()
config.readFile(inPath+"std_cfg.cfg")
cp = ConfigPusher(config, outPath)
for temp in np.linspace(3.0, 10.0, 4):
cp.initialize(nfcc=8, T=0.5, temperature = temp*2*3, v_dist = 0)
cp.thermalize(T = 2, temperature=temp, tau = 10.0)
cp.release(T=6.0)
"""
cp.initialize(nfcc = 8, T=0.5, temperature = 5.0, v_dist = 0)
for temp in [5.0, 4.5, 4.0, 3.5, 3.0, 3.5, 3.0, 2.5, 2.0, 1.5, 1.0, 0.5, 0.25, 0.125, 0.05, 0.01, 0.0]:
cp.thermalize(temperature=temp, tau = 10.0)
cp.release()
from pylibconfig import Config
import numpy as np
import matplotlib.pyplot as plt
import sys
def minimumDistance(r1, r2, L):
r_diff = r1-r2;
for i in xrange(3):
r_diff[i] = min(abs(r_diff[i]), L-abs(r_diff[i]))
return np.sqrt(np.dot(r_diff, r_diff))
path = "/home/henrik/NumericalData/FYS4460/2048_longrun/"
name = "mdsim0007"
infile_vmd = open(path+name +"/" +"out.xyz")
config = Config()
config.readFile(path+name+"/"+name+".cfg")
L = config.value("system.initialization.state.L")[0]
V = L**3;
num_particles = config.value("system.initialization.state.num_particles")[0]
#num_particles = 10
particle_positions = []
n_bins = 1000;
dr = L/(2*n_bins-1);
distance_densities = np.zeros(n_bins)
distances = np.linspace(dr, L/2+dr, n_bins)
cut1 = 2
cut2 = num_particles+2
