def missing_features(*args):
"""Returns a list of the missing features in the argument"""
if len(args) == 1 and not isinstance(args[0], str) and hasattr(args[0], "__iter__"):
return set(args[0]) - set(features())
return set(args) - set(features())
def has_features(*args):
"""Tests whether a list of features is a subset of the compiled-in features"""
if len(args) == 1 and not isinstance(args[0], str) and hasattr(args[0], "__iter__"):
return set(args[0]) < set(features())
return set(args) < set(features())
def test_has_features(self):
for feature in code_info.features():
self.assertTrue(has_features(feature))
for feature in code_info.all_features() - set(code_info.features()):
self.assertFalse(has_features(feature))
with self.assertRaises(RuntimeError) as _:
has_features("NotAFeature")
def has_features(*args):
"""Tests whether a list of features is a subset of the compiled-in features"""
if len(args) == 1 and not isinstance(args[0], str) and hasattr(
args[0], "__iter__"):
check_set = set(args[0])
else:
check_set = set(args)
if not check_set < all_features():
raise RuntimeError("'{}' is not a feature".format(
','.join(check_set - all_features())))
return check_set < set(features())
import espressomd._system as es
import espressomd
from espressomd import thermostat
from espressomd import code_info
from espressomd import analyze
from espressomd import integrate
from espressomd import lb
import numpy as np
print("""
=======================================================
= lbf.py =
=======================================================
Program Information:""")
print(code_info.features())
system = espressomd.System()
system.time_step = 0.01
system.skin = 0.1
box_l = 50
system.box_l =[box_l, box_l, box_l]
system.periodic = [1,1,1]
system.part.add(id=0, pos=[box_l/2.0,box_l/2.0,box_l/2.0], fix=[1,1,1])
# system.part.add(id=0, pos=[box_l/2.0,box_l/2.0,box_l/2.0], ext_force=[0,0,1])
lbf = lb.LBFluid(agrid=1, fric=1, dens=1, visc=1, tau=0.01, ext_force=[0,0,-1.0/(box_l**3)])
system.actors.add(lbf)
import espressomd
from espressomd import thermostat
from espressomd import code_info
from espressomd import analyze
from espressomd import integrate
from espressomd import electrostatics
from espressomd import electrostatic_extensions
import numpy
print("""
=======================================================
= p3m.py =
=======================================================
Program Information:""")
print(code_info.features())
dev = "cpu"
# System parameters
#############################################################
# 10 000 Particles
box_l = 10.7437
density = 0.7
# Interaction parameters (repulsive Lennard Jones)
#############################################################
lj_eps = 1.0
lj_sig = 1.0
self.assertTrue(self.bondsMatch(tnIn,tnOut,params,outParams), bondClass(**params).typeName()+": value set and value gotten back differ for bond id "+str(bondId)+": "+params.__str__()+" vs. "+outParams.__str__())
return func
def test_aa_bondedInterSetterGetter(self):
self.system.bondedInter[0]=HarmonicBond(k=0,r_0=0)
bond=self.system.bondedInter[0]
self.assertTrue(isinstance(bond,HarmonicBond),"The bond was created as harmonic bond but the instance gotten back is of different type.")
test_fene = generateTestForBondParams(0,FeneBond,{"r_0":1.1, "k":5.2, "d_r_max":3.})
test_fene2 = generateTestForBondParams(1,FeneBond,{"r_0":1.1, "k":5.2, "d_r_max":3.})
test_harmonic = generateTestForBondParams(0,HarmonicBond,{"r_0":1.1, "k":5.2})
test_harmonic2 = generateTestForBondParams(0,HarmonicBond,{"r_0":1.1, "k":5.2, "r_cut":1.3})
test_dihedral = generateTestForBondParams(0,Dihedral,{"mult":3.0, "bend":5.2,"phase":3.})
test_angle_harm = generateTestForBondParams(0,Angle_Harmonic,{"bend":5.2, "phi0":3.2})
test_angle_cos = generateTestForBondParams(0,Angle_Cosine,{"bend":5.2, "phi0":3.2})
test_angle_cossquare = generateTestForBondParams(0,Angle_Cossquare,{"bend":5.2, "phi0":0.})
test_subt_lj = generateTestForBondParams(0,Subt_Lj,{"k":5.2, "r":3.2})
test_stretching_force = generateTestForBondParams(0,Stretching_Force,{"r0":5.2, "ks":3.2})
test_area_force_local = generateTestForBondParams(0,Area_Force_Local,{"A0_l":5.2, "ka_l":3.2})
test_bending_force = generateTestForBondParams(0,Bending_Force,{"phi0":5.2, "kb":3.2})
test_volume_force = generateTestForBondParams(0,Volume_Force,{"V0":5.2, "kv":3.2})
test_area_force_global = generateTestForBondParams(0,Area_Force_Global,{"A0_g":5.2, "ka_g":3.2})
test_stretchlin_force = generateTestForBondParams(0,Stretchlin_Force,{"r0":5.2, "kslin":3.2})
if __name__ == "__main__":
print("Features: ",code_info.features())
ut.main()
class ParticleProperties(ut.TestCase):
# def __init__(self,particleId):
# self.pid=particleId
# the system which will be tested
system = espressomd.System()
# Particle id to work on
pid = 17
# Error tolerance when comparing arrays/tuples...
tol = 1E-9
def bondsMatch(self, inType, outType, inParams, outParams):
"""Check, if the bond type set and gotten back as well as the bond
parameters set and gotten back match. Only check keys present in
inParams.
"""
if inType != outType:
return False
for k in list(inParams.keys()):
if k not in outParams:
return False
if outParams[k] != inParams[k]:
return False
return True
def setUp(self):
if not self.system.part.exists(self.pid):
self.system.part.add(id=self.pid, pos=(0, 0, 0, 0))
def generateTestForBondParams(_bondId, _bondClass, _params):
"""Generates test cases for checking bond parameters set and gotten back
from Es actually match. Only keys which are present in _params are checked
1st arg: Id of the bonded ia in Espresso to test on, i.e., 0,2,1...
2nd: Class of the bond potential to test, ie.e, FeneBond, HarmonicBond
3rd: Bond parameters as dictionary, i.e., {"k"=1.,"r_0"=0.
"""
bondId = _bondId
bondClass = _bondClass
params = _params
def func(self):
# This code is run at the execution of the generated function.
# It will use the state of the variables in the outer function,
# which was there, when the outer function was called
self.system.bonded_inter[bondId] = bondClass(**params)
outBond = self.system.bonded_inter[bondId]
tnIn = bondClass(**params).type_number()
tnOut = outBond.type_number()
outParams = outBond.params
self.assertTrue(
self.bondsMatch(tnIn, tnOut, params, outParams),
bondClass(**params).type_name() +
": value set and value gotten back differ for bond id " +
str(bondId) + ": " + params.__str__() + " vs. " +
outParams.__str__())
return func
test_fene = generateTestForBondParams(0, FeneBond, {
"r_0": 1.1,
"k": 5.2,
"d_r_max": 3.
})
test_fene2 = generateTestForBondParams(1, FeneBond, {
"r_0": 1.1,
"k": 5.2,
"d_r_max": 3.
})
test_harmonic = generateTestForBondParams(0, HarmonicBond, {
"r_0": 1.1,
"k": 5.2
})
test_harmonic2 = generateTestForBondParams(0, HarmonicBond, {
"r_0": 1.1,
"k": 5.2,
"r_cut": 1.3
})
if "ROTATION" in code_info.features():
test_harmonic_dumbbell = generateTestForBondParams(
0, HarmonicDumbbellBond, {
"k1": 1.1,
"k2": 2.2,
"r_0": 1.5
})
test_harmonic_dumbbell2 = generateTestForBondParams(
0, HarmonicDumbbellBond, {
"k1": 1.1,
"k2": 2.2,
"r_0": 1.5,
"r_cut": 1.9
})
test_dihedral = generateTestForBondParams(0, Dihedral, {
"mult": 3.0,
"bend": 5.2,
"phase": 3.
})
if "BOND_ANGLE" in espressomd.features():
test_angle_harm = generateTestForBondParams(0, Angle_Harmonic, {
"bend": 5.2,
"phi0": 3.2
})
test_angle_cos = generateTestForBondParams(0, Angle_Cosine, {
"bend": 5.2,
"phi0": 3.2
})
test_angle_cossquare = generateTestForBondParams(
0, Angle_Cossquare, {
"bend": 5.2,
"phi0": 0.
})
if "LENNARD_JONES" in espressomd.features():
test_subt_lj = generateTestForBondParams(0, Subt_Lj, {
"k": 5.2,
"r": 3.2
})
if "TABULATED" in espressomd.features():
test_tabulated = generateTestForBondParams(0, Tabulated, {
"type": "distance",
"filename": "lj1.tab"
})
if "BOND_ANGLE" in espressomd.features():
test_angle_harm = generateTestForBondParams(0, Angle_Harmonic, {
"bend": 5.2,
"phi0": 3.2
})
test_angle_cos = generateTestForBondParams(0, Angle_Cosine, {
"bend": 5.2,
"phi0": 3.2
})
test_angle_cossquare = generateTestForBondParams(
0, Angle_Cossquare, {
"bend": 5.2,
"phi0": 0.
})
if "LENNARD_JONES" in espressomd.features():
test_subt_lj = generateTestForBondParams(0, Subt_Lj, {
"k": 5.2,
"r": 3.2
})
if "TABULATED" in espressomd.features():
test_tabulated = generateTestForBondParams(0, Tabulated, {
"type": "distance",
"filename": "lj1.tab"
})
if __name__ == "__main__":
print("Features: ", code_info.features())
ut.main()
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
from __future__ import print_function
import espressomd._system as es
import espressomd
from espressomd import thermostat
from espressomd import code_info
import numpy as np
print("""
=======================================================
= slice_input.py =
=======================================================
Program Information:""")
print(code_info.features())
dev = "cpu"
# System parameters
#############################################################
box_l = 10.0
# Integration parameters
#############################################################
system = espressomd.System()
system.time_step = 0.01
system.cell_system.skin = 0.4
#
from __future__ import print_function
import espressomd._system as es
import espressomd
from espressomd import code_info
from espressomd import electrostatics
from espressomd import electrostatic_extensions
import numpy
print("""
=======================================================
= store_properties.py =
=======================================================
Program Information:""")
print(code_info.features())
if not "ELECTROSTATICS" in code_info.features():
raise Exception("Sample script requires ELECTROSTATICS")
dev = "cpu"
# System parameters
#############################################################
# 10 000 Particles
box_l = 10.7437
density = 0.7
# Interaction parameters (repulsive Lennard Jones)
#############################################################
import espressomd._system as es
import espressomd
from espressomd import thermostat
from espressomd import code_info
from espressomd import integrate
from espressomd import electrostatics
from espressomd import electrostatic_extensions
import numpy
print("""
=======================================================
= store_properties.py =
=======================================================
Program Information:""")
print(code_info.features())
if not "ELECTROSTATICS" in code_info.features():
raise Exception("Sample script requires ELECTROSTATICS")
dev = "cpu"
# System parameters
#############################################################
# 10 000 Particles
box_l = 10.7437
density = 0.7
# Interaction parameters (repulsive Lennard Jones)
#############################################################
if method not in implemented_methods:
print("Please select an electrostatics method in the script.")
exit()
# Distinguish between different methods
if method == "p3m":
p3m = electrostatics.P3M(bjerrum_length=10.0, accuracy=1e-3)
system.actors.add(p3m)
print("P3M parameter:\n")
p3m_params = p3m.get_params()
for key in p3m_params.keys():
print("{} = {}".format(key, p3m_params[key]))
# elif method == "memd":
# TODO
if "ROTATION" in code_info.features():
deg_free = 6
else:
deg_free = 3
# Integration parameters
integ_steps = 200
int_n_times = 20
# Warmup integration loop
print("\nWarmup")
for cap in xrange(20, 200, 20):
print("t={0}, E={1}".format(system.time,
system.analysis.energy()['total']))
system.non_bonded_inter.set_force_cap(cap)
integrate.integrate(integ_steps)