def convertToS(self, mol, activeS):
# First get S
S = ct.getDistMatrix(mol, activeS)
if self.sInd == 0:
self.sInd = S[1]
self.reac = S[0]
try:
Snorm, project, node, dist = ct.projectPointOnPath(
S[0], self.path, self.pathType,
self.boxList[self.box].lower.norm,
self.boxList[self.box].lower.D, self.reac, self.pathNode,
self.reverse)
except:
Snorm = 0
project = 0
node = False
dist = 0
return S[0], Snorm, project, node, dist
def run(gl):
#Read reactant definition
if gl.StartType == 'file':
Reac = read(gl.Start)
elif gl.StartType == 'Smile':
Reac = tl.getMolFromSmile(gl.Start)
#Read product definition
if gl.EndType == 'file':
Prod= read(gl.End)
elif gl.EndType == 'Smile':
Prod = tl.getMolFromSmile(gl.End)
#Set calculatiors
#Reac = tl.setCalc(Reac,"DOS/", gl.trajMethod, gl.atomTypes)
if gl.trajMethod == "openMM":
Reac = tl.setCalc(Reac,"GenBXD/", gl.trajMethod, gl)
else:
Reac = tl.setCalc(Reac,"GenBXD/", gl.trajMethod, gl.trajLevel)
Prod = tl.setCalc(Prod,"GenBXD/", gl.trajMethod, gl.trajLevel)
# Partially minimise both reactant and product
if gl.GenBXDrelax:
min = BFGS(Reac)
try:
min.run(fmax=0.1, steps=20)
except:
min.run(fmax=0.1, steps=20)
min2 = BFGS(Prod)
try:
min2.run(fmax=0.1, steps=20)
except:
min2.run(fmax=0.1, steps=20)
# Get important interatomic distances
if gl.CollectiveVarType == "changedBonds":
cbs = ct.getChangedBonds2(Reac, Prod)
elif gl.CollectiveVarType == "all":
cbs = ct.getChangedBonds2(Reac, Prod)
elif gl.CollectiveVarType == "specified":
cbs = gl.CollectiveVar
elif gl.CollectiveVarType == "file":
cbs = gl.principalCoordinates
#Get path to project along
distPath = []
totalPathLength = 0
if gl.PathType == 'curve' or gl.PathType == 'gates':
if gl.PathFile == 'none':
Path = getPath(Reac,Prod,gl)
else:
Path = read(gl.PathFile,index=('::'+str(gl.pathStride)))
distPath.append((ct.getDistMatrix(Path[0],cbs)[0],0))
for i in range(1,len(Path)):
l = np.linalg.norm(ct.getDistMatrix(Path[i],cbs)[0] - ct.getDistMatrix(Path[i-1], cbs)[0])
totalPathLength += l
distPath.append((ct.getDistMatrix(Path[i],cbs)[0],totalPathLength))
elif gl.PathType == 'linear':
distPath = ct.getDistMatrix(Prod,cbs)[0] - ct.getDistMatrix(Reac, cbs)[0]
if gl.PathType == 'curve' or gl.PathType == 'gates':
pathFile = open('reducedPath.txt','w')
for p in distPath:
pathFile.write('s = ' + str(p[0]) + '\n')
pathFile.close()
# initialise then run trajectory
t = Trajectory.Trajectory(Reac,gl,os.getcwd(),0,False)
t.runGenBXD(Reac,Prod,gl.maxHits,gl.maxAdapSteps,gl.PathType,distPath, cbs, gl.decorrelationSteps, gl.histogramBins,totalPathLength, gl.fixToPath, gl.pathDistCutOff,gl.epsilon)