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Commit 5f029cad authored by Giovanni Bussi's avatar Giovanni Bussi
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Using nosetests correctly 

there should be a function called test(), otherwise nose just imports
the modules and thinks no test was done
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python/test/test_run.py
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...@@ -39,8 +39,6 @@ ...@@ -39,8 +39,6 @@
import numpy as np import numpy as np
import plumed import plumed
import os import os
os.chdir('test/')
os.system('rm -f bck.*')
def read_xyz(filename): def read_xyz(filename):
xyz = open(filename) xyz = open(filename)
...@@ -70,83 +68,90 @@ def create_plumed_var( p, name, command ): ...@@ -70,83 +68,90 @@ def create_plumed_var( p, name, command ):
p.cmd("setMemoryForData " + name, data ) p.cmd("setMemoryForData " + name, data )
return data return data
# Output to four decimal places only def test():
np.set_printoptions(precision=4) os.chdir('test/')
# Read trajectory os.system('rm -f bck.*')
traj = read_xyz("traj.xyz") # Output to four decimal places only
num_frames = len(traj) np.set_printoptions(precision=4)
num_atoms = traj[0].shape[0] # Read trajectory
traj = read_xyz("traj.xyz")
num_frames = len(traj)
num_atoms = traj[0].shape[0]
# Create arrays for stuff
box=np.diag(12.41642*np.ones(3,dtype=np.float64))
virial=np.zeros((3,3),dtype=np.float64)
masses=np.ones(num_atoms,dtype=np.float64)
forces=np.random.rand(num_atoms,3)
charges=np.zeros(num_atoms,dtype=np.float64)
# Create PLUMED object and read input
p = plumed.Plumed()
p.cmd("setMDEngine","python")
p.cmd("setTimestep", 1.)
p.cmd("setKbT", 1.)
p.cmd("setNatoms",num_atoms)
p.cmd("setLogFile","test.log")
p.cmd("init")
p.cmd("readInputLine","MOLINFO STRUCTURE=template.pdb")
t1 = create_plumed_var( p, "t1", "TORSION ATOMS=@phi-2" )
t2 = create_plumed_var( p, "t2", "TORSION ATOMS=@psi-2" )
t3 = create_plumed_var( p, "t3", "TORSION ATOMS=@phi-3" )
t4 = create_plumed_var( p, "t4", "TORSION ATOMS=@psi-3" )
t5 = create_plumed_var( p, "t5", "TORSION ATOMS=@phi-4" )
t6 = create_plumed_var( p, "t6", "TORSION ATOMS=@psi-4" )
t7 = create_plumed_var( p, "t7", "TORSION ATOMS=@phi-5" )
t8 = create_plumed_var( p, "t8", "TORSION ATOMS=@psi-5" )
t9 = create_plumed_var( p, "t9", "TORSION ATOMS=@phi-6" )
t10 = create_plumed_var( p, "t10", "TORSION ATOMS=@psi-6" )
t11 = create_plumed_var( p, "t11", "TORSION ATOMS=@phi-7" )
t12 = create_plumed_var( p, "t12", "TORSION ATOMS=@psi-7" )
t13 = create_plumed_var( p, "t13", "TORSION ATOMS=@phi-8" )
t14 = create_plumed_var( p, "t14", "TORSION ATOMS=@psi-8" )
t15 = create_plumed_var( p, "t15", "TORSION ATOMS=@phi-9" )
t16 = create_plumed_var( p, "t16", "TORSION ATOMS=@psi-9" )
t17 = create_plumed_var( p, "t17", "TORSION ATOMS=@phi-10" )
t18 = create_plumed_var( p, "t18", "TORSION ATOMS=@psi-10" )
t19 = create_plumed_var( p, "t19", "TORSION ATOMS=@phi-11" )
t20 = create_plumed_var( p, "t20", "TORSION ATOMS=@psi-11" )
t21 = create_plumed_var( p, "t21", "TORSION ATOMS=@phi-12" )
t22 = create_plumed_var( p, "t22", "TORSION ATOMS=@psi-12" )
t23 = create_plumed_var( p, "t23", "TORSION ATOMS=@phi-13" )
t24 = create_plumed_var( p, "t24", "TORSION ATOMS=@psi-13" )
t25 = create_plumed_var( p, "t25", "TORSION ATOMS=@phi-14" )
t26 = create_plumed_var( p, "t26", "TORSION ATOMS=@psi-14" )
t27 = create_plumed_var( p, "t27", "TORSION ATOMS=@phi-15" )
t28 = create_plumed_var( p, "t28", "TORSION ATOMS=@psi-15" )
t29 = create_plumed_var( p, "t29", "TORSION ATOMS=@phi-16" )
t30 = create_plumed_var( p, "t30", "TORSION ATOMS=@psi-16" )
t31 = create_plumed_var( p, "t31", "TORSION ATOMS=@phi-17" )
t32 = create_plumed_var( p, "t32", "TORSION ATOMS=@psi-17" )
# Read in the correct answers that were calculated directly using PLUMED
correct_torsions = np.loadtxt("colvar.ref")
# Open an output file
of = open("logfile", "w+")
# Now analyze the trajectory
for step in range(0,num_frames) :
of.write("RUNNING ANALYSIS FOR STEP " + str(step) + "\n" )
p.cmd("setStep",step )
p.cmd("setBox",box )
p.cmd("setMasses", masses )
p.cmd("setCharges", charges )
p.cmd("setPositions", traj[step])
p.cmd("setForces", forces )
p.cmd("setVirial", virial )
p.cmd("calc")
bias = np.zeros((1),dtype=np.float64)
p.cmd("getBias", bias )
variables = np.array([t1,t2,t3,t4,t5,t6,t7,t8,t9,t10,t11,t12,t13,t14,t15,t16,t17,t18,t19,t20,t21,t22,t23,t24,t25,t26,t27,t28,t29,t30,t31,t32]).ravel()
zeros = variables - correct_torsions[step,1:]
for data in zeros :
if abs(data)>1E-4 : of.write("MISMATCH BETWEEN VALUE FROM PLUMED AND VALUE FROM PYTHON")
of.close()
# Create arrays for stuff if __name__ == "__main__":
box=np.diag(12.41642*np.ones(3,dtype=np.float64)) test()
virial=np.zeros((3,3),dtype=np.float64)
masses=np.ones(num_atoms,dtype=np.float64)
forces=np.random.rand(num_atoms,3)
charges=np.zeros(num_atoms,dtype=np.float64)
# Create PLUMED object and read input
p = plumed.Plumed()
p.cmd("setMDEngine","python")
p.cmd("setTimestep", 1.)
p.cmd("setKbT", 1.)
p.cmd("setNatoms",num_atoms)
p.cmd("setLogFile","test.log")
p.cmd("init")
p.cmd("readInputLine","MOLINFO STRUCTURE=template.pdb")
t1 = create_plumed_var( p, "t1", "TORSION ATOMS=@phi-2" )
t2 = create_plumed_var( p, "t2", "TORSION ATOMS=@psi-2" )
t3 = create_plumed_var( p, "t3", "TORSION ATOMS=@phi-3" )
t4 = create_plumed_var( p, "t4", "TORSION ATOMS=@psi-3" )
t5 = create_plumed_var( p, "t5", "TORSION ATOMS=@phi-4" )
t6 = create_plumed_var( p, "t6", "TORSION ATOMS=@psi-4" )
t7 = create_plumed_var( p, "t7", "TORSION ATOMS=@phi-5" )
t8 = create_plumed_var( p, "t8", "TORSION ATOMS=@psi-5" )
t9 = create_plumed_var( p, "t9", "TORSION ATOMS=@phi-6" )
t10 = create_plumed_var( p, "t10", "TORSION ATOMS=@psi-6" )
t11 = create_plumed_var( p, "t11", "TORSION ATOMS=@phi-7" )
t12 = create_plumed_var( p, "t12", "TORSION ATOMS=@psi-7" )
t13 = create_plumed_var( p, "t13", "TORSION ATOMS=@phi-8" )
t14 = create_plumed_var( p, "t14", "TORSION ATOMS=@psi-8" )
t15 = create_plumed_var( p, "t15", "TORSION ATOMS=@phi-9" )
t16 = create_plumed_var( p, "t16", "TORSION ATOMS=@psi-9" )
t17 = create_plumed_var( p, "t17", "TORSION ATOMS=@phi-10" )
t18 = create_plumed_var( p, "t18", "TORSION ATOMS=@psi-10" )
t19 = create_plumed_var( p, "t19", "TORSION ATOMS=@phi-11" )
t20 = create_plumed_var( p, "t20", "TORSION ATOMS=@psi-11" )
t21 = create_plumed_var( p, "t21", "TORSION ATOMS=@phi-12" )
t22 = create_plumed_var( p, "t22", "TORSION ATOMS=@psi-12" )
t23 = create_plumed_var( p, "t23", "TORSION ATOMS=@phi-13" )
t24 = create_plumed_var( p, "t24", "TORSION ATOMS=@psi-13" )
t25 = create_plumed_var( p, "t25", "TORSION ATOMS=@phi-14" )
t26 = create_plumed_var( p, "t26", "TORSION ATOMS=@psi-14" )
t27 = create_plumed_var( p, "t27", "TORSION ATOMS=@phi-15" )
t28 = create_plumed_var( p, "t28", "TORSION ATOMS=@psi-15" )
t29 = create_plumed_var( p, "t29", "TORSION ATOMS=@phi-16" )
t30 = create_plumed_var( p, "t30", "TORSION ATOMS=@psi-16" )
t31 = create_plumed_var( p, "t31", "TORSION ATOMS=@phi-17" )
t32 = create_plumed_var( p, "t32", "TORSION ATOMS=@psi-17" )
# Read in the correct answers that were calculated directly using PLUMED
correct_torsions = np.loadtxt("colvar.ref")
# Open an output file
of = open("logfile", "w+")
# Now analyze the trajectory
for step in range(0,num_frames) :
of.write("RUNNING ANALYSIS FOR STEP " + str(step) + "\n" )
p.cmd("setStep",step )
p.cmd("setBox",box )
p.cmd("setMasses", masses )
p.cmd("setCharges", charges )
p.cmd("setPositions", traj[step])
p.cmd("setForces", forces )
p.cmd("setVirial", virial )
p.cmd("calc")
bias = np.zeros((1),dtype=np.float64)
p.cmd("getBias", bias )
variables = np.array([t1,t2,t3,t4,t5,t6,t7,t8,t9,t10,t11,t12,t13,t14,t15,t16,t17,t18,t19,t20,t21,t22,t23,t24,t25,t26,t27,t28,t29,t30,t31,t32]).ravel()
zeros = variables - correct_torsions[step,1:]
for data in zeros :
if abs(data)>1E-4 : of.write("MISMATCH BETWEEN VALUE FROM PLUMED AND VALUE FROM PYTHON")
of.close()
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