def test_it():
myinfilename = os.path.join(os.path.dirname(__file__), 'traj_fit.xtc')
myintopname = os.path.join(os.path.dirname(__file__), 'reference.pdb')
mycolvarname = os.path.join(os.path.dirname(__file__), 'results_isomap')
ae, cor = anncolvar.anncollectivevariable(infilename=myinfilename,
intopname=myintopname,
colvarname=mycolvarname,
column=2,
boxx=1.0,
boxy=1.0,
boxz=1.0,
atestset=0.1,
shuffle=1,
nofit=0,
layers=3,
layer1=16,
layer2=8,
layer3=4,
actfun1='sigmoid',
actfun2='sigmoid',
actfun3='sigmoid',
optim='adam',
loss='mean_squared_error',
epochs=1000,
batch=256,
ofilename='',
modelfile='',
plumedfile='')
assert (cor > 0.99)
def test_it():
myinfilename = os.path.join(os.path.dirname(__file__), 'traj_fit.xtc')
myintopname = os.path.join(os.path.dirname(__file__), 'reference.pdb')
mycolvarname = os.path.join(os.path.dirname(__file__), 'results_isomap')
myplumedname = os.path.join(os.path.dirname(__file__), 'test.dat')
myplumedname2 = os.path.join(os.path.dirname(__file__), 'test2.dat')
ae, cor = anncolvar.anncollectivevariable(infilename=myinfilename,
intopname=myintopname,
colvarname=mycolvarname,
column=2,
boxx=1.0,
boxy=1.0,
boxz=1.0,
atestset=0.1,
shuffle=1,
nofit=0,
layers=1,
layer1=16,
layer2=8,
layer3=4,
actfun1='tanh',
actfun2='linear',
actfun3='linear',
optim='adam',
loss='mean_squared_error',
epochs=1000,
batch=256,
ofilename='',
modelfile='',
plumedfile=myplumedname,
plumedfile2=myplumedname2)
command = "plumed driver --mf_pdb " + myintopname + " --plumed " + myplumedname
now = dt.datetime.now()
os.system(command)
print("time %i s\n" % (dt.datetime.now() - now).seconds)
ifile = open("COLVAR", "r").readlines()
sline = str.split(ifile[1])
x = float(sline[1])
assert ((x > 0.29) and (x < 0.33))