diff --git a/python/test/test_run.py b/python/test/test_run.py
index 63d8e68dbab39795221c5794d1c271a3784d58da..0408b373a1a4aa97743e3a48bdfa983240d29b7f 100644
--- a/python/test/test_run.py
+++ b/python/test/test_run.py
@@ -39,8 +39,6 @@
import numpy as np
import plumed
import os
-os.chdir('test/')
-os.system('rm -f bck.*')
def read_xyz(filename):
xyz = open(filename)
@@ -70,83 +68,90 @@ def create_plumed_var( p, name, command ):
p.cmd("setMemoryForData " + name, data )
return data
-# Output to four decimal places only
-np.set_printoptions(precision=4)
-# Read trajectory
-traj = read_xyz("traj.xyz")
-num_frames = len(traj)
-num_atoms = traj[0].shape[0]
+def test():
+ os.chdir('test/')
+ os.system('rm -f bck.*')
+ # Output to four decimal places only
+ np.set_printoptions(precision=4)
+ # 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
-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)
+if __name__ == "__main__":
+ test()
-# 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()