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))