diff --git a/mrdna/model/arbdmodel.py b/mrdna/model/arbdmodel.py index 81ce94e61a1c1087f12320d608c1f2bbff4aa540..3d565f08e96f6a0353dff6cf9bf414ec3963b816 100644 --- a/mrdna/model/arbdmodel.py +++ b/mrdna/model/arbdmodel.py @@ -733,7 +733,7 @@ class ArbdModel(PdbModel): def writeArbdFiles(self, prefix, numSteps=100000000, outputPeriod=10000): ## TODO: save and reference directories and prefixes using member data - d = "potentials" + d = self.potential_directory = "potentials" if not os.path.exists(d): os.makedirs(d) self._bond_filename = "%s/%s.bonds.txt" % (d, prefix) @@ -834,7 +834,7 @@ diffusion {diffusivity} fh.write("gridFileScale {}\n".format(gridFileScale)) else: - fh.write("gridFile null.dx\n") + fh.write("gridFile {}/null.dx\n".format(self.potential_directory)) ## Write coordinates and interactions fh.write(""" @@ -876,7 +876,8 @@ tabulatedPotential 1 write_null_dx = False for pt,num in self.getParticleTypesAndCounts(): if "grid" not in pt.__dict__: - with open("null.dx",'w') as fh: + gridfile = "{}/null.dx".format(self.potential_directory) + with open(gridfile, 'w') as fh: fh.write("""object 1 class gridpositions counts 2 2 2 origin {originX} {originY} {originZ} delta {dimX} 0.000000 0.000000