Faster-Math should have current Development Branch Code #310
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…outputted. The keyword for config file to read in the binary coordinate is: "binCoordinates BoxNumber FileName.coor". The keyword for config file to read in the extended system file is: "extendedSystem BoxNumber FileName.xsc"
Read in restart binary coordinate and extended system file
Reading Multi parameter files
redirect error when intel not present #262
Fix to ERROR: Error closing DCD file` at the end of simulation
…tials of the same molecule, i.e. our H20 and h2o example. Also, added error check that will prevent segfaults when number of atoms in psf != number of atoms in pdb
Added atom equality operator to allow for user defined chemical poten…
Simplified the logic between two box psf parser.
Added googletest
Fixed psf restart headers
…dy for NAMD testing.
Prints actual residue for proteins in PDB Restart file. Should be re…
…rs, nnb, ngrp). Also added some logic to parse a second psf file if we need it, instead of relying on the restart flag to tell us how many psf flags to parse. We only parse if the first psf file we readed doesn't contain all the atoms in the pdb file, (also a second psf file has to exist).
added the extra terms namd requires at the end of a psf file (imprope…
Fixed checkpoint system
…phene where atoms are named c1, c2, c3...etc. All the same type, mass, charge, ect. Still having problems rectifying new parser which uses bonds to determine molecules, with a bondless molecule like graphene. We represent graphene as bondless. Perhaps, we could create bonds b/w carbon molecules.
Probabilities and Coefficients are calculated using only swappable molecules for molecule transfer and MEMC.
… resID as an index into startIdxRes
PSF Parser can handle MosDef format Porous Materials
Revert "Merge pull request #304 from GregorySchwing/rebasedpsfparsert…
…molecules, only using pdb for beta, coords, and chains. Then, I patched the pdb and psf outputs for multiresidue and single molecules. Particular attention paid to deprecate the use of residue ID from pdb for determining molecule information.
…liases. Still figuring out chain and segment
…le to use molecule and not residue for Mol_frac
…number of variables and prevent printing in different order than kindMap. Not a huge concern retrospectively
…t test for GetConsensusBeta, and the order of strength for determining molBeta is 1 > 2 > 0
split psf and pdb parsers. We only use psf for determining number of…
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Faster-Math should have current Development Branch Code