def writeSeries(oldInput, key, replacements, GPU=False):
mainDir = basename(oldInput).split(".")[0] + "series"
mkdir(mainDir)
for repl in replacements:
newDir = "step" + str(repl)
newDir = join(mainDir, newDir)
mkdir(newDir)
inputName = join(newDir, "step" + str(repl) + ".com")
rewriteInput(oldInput, inputName, key, repl)
writeSlurmScript(join(newDir, "run.slurm"), basename(inputName), GPU)
def writeScans( oldInput, coords, atomStart, atom2Move, atomDir, nSteps, minDist, GPU = False ):
atomStartIndex = atomStart
atomStart = np.array(coords[atom2Move])
atomStop = np.array(coords[atomDir])
moveVector = atomStop - atomStart
length = np.linalg.norm(moveVector)
moveVector = moveVector*(length-minDist)/length
step = moveVector/nSteps
mainDir = basename(oldInput).split(".")[0]+"scan"
mkdir(mainDir)
for i in range(nSteps):
newDir = "step"+str(i)
newDir = join(mainDir, newDir)
mkdir(newDir)
atomStart += step
coords[atom2Move] = atomStart.tolist()
inputName = join(newDir, "step"+str(i)+".com")
writeNewInput(oldInput, coords, inputName, "" )
writeSlurmScript(join(newDir, "run.slurm"), basename(inputName), GPU)
inpFile = join(dirname, dirname + ".inp")
inputFile = open(inpFile, 'w')
xyzName = basename(xyzFile)
inputFile.write("basis 6-31g**\n")
inputFile.write("charge 0\n")
inputFile.write("run ts\n")
inputFile.write("method ub3lyp\n")
inputFile.write("new_minimizer yes\n")
inputFile.write("coordinates " + xyzName + "\nend\n\n")
frozen = []
for f in indexes:
frozen.append(str(f + 1))
if frozen:
inputFile.write("$constraint_freeze\n")
if frozen:
inputFile.write("xyz " + ",".join(frozen) + "\n")
inputFile.write("$end\n")
inputFile.close()
writeSlurmScript(join(dirname, dirname + ".slurm"), basename(inpFile),
True, "terachem")
else:
print("katalog " + dirname + " juz istnieje")
line = oldFile.readline()
destiny.close()
oldFile.close()
if len(sys.argv) < 4:
print(
"Potrzebuje: g16Log, oldInput, newInputName, geometry index [optional, negative indexes possible]"
)
else:
g16Log = sys.argv[1]
oldInput = sys.argv[2]
newInputName = sys.argv[3]
index = -1
if len(sys.argv) > 4:
index = int(sys.argv[4])
newDir = newInputName.split(".")[0]
if isdir(newDir):
print("Wybrana sciezka juz istnieje!")
else:
mkdir(newDir)
last = getCoordsFromLog(g16Log, index)
newInputName = join(newDir, newInputName)
writeNewInput(oldInput, last, newInputName)
writeSlurmScript(join(newDir, "run.slurm"), basename(newInputName),
False)
destiny.write(line)
line = oldFile.readline()
destiny.close()
oldFile.close()
if len(sys.argv) < 3:
print("Potrzebuje: input start, input final, steps, gpu(optional)")
else:
inputStart = sys.argv[1]
inputFinal = sys.argv[2]
steps = int(sys.argv[3])
gpu = False
if len(sys.argv) > 4:
gpu = True
indexesStart, coordsStart, el = getFrozenIndexes(inputStart)
indexesFinal, coordsFinal, el = getFrozenIndexes(inputFinal)
coordsFinalFixed = fixCoordinates(indexesStart, coordsStart, coordsFinal)
frames = generateFrames(coordsStart, coordsFinalFixed, steps)
for n, frame in enumerate(frames):
dirname = "linerScan_" + str(n)
mkdir(dirname)
inputName = join(dirname, "linearScan.com")
slurmFile = join(dirname, "linearScan.slurm")
writeNewInput(inputStart, frame, inputName)
writeSlurmScript(slurmFile, basename(inputName), gpu)