Setup History
v3.6.1 v3.8.2 v3.9.0 v3.9.6
v4.1.3 v4.1.6
v5.0 v5.1 v5.2 v5.2.1
v5.2.1
Date Description
--------------------------------------------------------------------------------------
20250801 - Web publication
20250715 - Repaired radius of gyration (gyration) and mean-squared displacement (msd)
sampling with LAMMPS
20250702 - Repaired -emc_export smiles
20250422 - Addition of -md_engine
- Addition of GROMACS hooks
20250318 - New subversion: 5.2.1
- Addition of polymeric groups
- Addition of -polymer_link to support of polymeric groups
20250215 - Addition of -xyz and derivatives for .xyz output
20241212 - Addition of -pdb_licorice for VMD licorice representation
20241005 - Added options -lammps_dump_box for including box multiples in
- LAMMPS trajectory files, -field_inverse for field inverse cut off, all
-gromacs for GROMACS port related settings,
-polymer_flory and -polymer_poisson for setting global defaults, and
-queue_bind for processor binding policies on compute nodes
20241001 - New version: 5.2
20240801 - Web publication
20240711 - Corrected Green-Kubo viscosity calculation
20240617 - Addition of MARTINI3
- Additions for template use in force fields
20240522 - Reversed the occurence of field location references
20240324 - Addition of #include to preprocessing
20240319 - Updated behavior with CHARMM CMAP files
20240214 - Repaired issues with ITEM EMC and LAMMPS
20240109 - Added '\' as line extensions (in addition to '&')
- Repaired group connectivity issues
- Repaired cluster ending in resulting EMC build scripts
20240103 - Repaired issues with -nchains
20231101 - New version: 5.1
- Added select to group connectivity for grafting purposes
20231003 - Updated -emc_moves by improving EMC::Hash::set() and text()
20230905 - Added -scratch and -sync for using local compute node storage
20230801 - Fixed quotation of loop sequenced variables by adding sequence check
EMC::Environment::job_loop_sequence_q()
20230701 - Fixed use of item variables in environment mode
20230611 - Improved variable interpretation in bash script loops
- Repaired preprocessing
20230316 - Altered run_sh() in write_job_functions() to reflect using third line from
last of run.sh output for obtaining job id
20230101 - New version: 5.0
- Full modularization
20220830 - Migration of list() to EMC::Hash::text() and set_list() to
EMC::Hash::set()
20220806 - New version: 4.1.4
- Improved behavior of ITEM INCLUDE
- Allowing for clusters to have the same name as polymeric groups
20220801 - Web publication
20220727 - Added map keyword to cluster import
20220407 - Importing DPD references through get_data_quick()
20220330 - New version: 4.1.3
- Added $::EMC::Lammps{newer_version} to use neighbor list style multi/old
for versions newer that 2020 through option -lammps
- Updated option -modules to [command=]module and inclusion into run.sh
- Improved packing mechanism of multiple jobs on one node
20220324 - Corrected use of sequences in loops
20220316 - Added type=system to import of structures
20220224 - Correction to parameter interpretation
- Preprocessing only when specifically set under environment
- Updated default coarse-graining coulombic parameters
- Gaussian bond constants set to k=5 and l=0
20220223 - Added rmax to -cutoff for use with gauss field
20220216 - Ironed out preprocessing issues with line extenders & and \
- Refined error on missing polymer definitions
20220207 - Fixed polymer type setting for included polymers
20220203 - Adapted -shake interpretation
20220131 - New version: 4.1.2
- Added gauss as force field; defaults set similar to dpd
- Added the use of the C preprocessor
20220118 - Updated split_data() and get_data() routines
- Added new get_data_quick() routine for reading parameters
20220112 - Fixed issues with with paired loop variables in bash scripts
- Added permutations to loop variables with extensions :2, :3, and :4
20220107 - Fixed issue with bash script variable names
20211129 - New version: 4.1.1
- Updated behavior for defining polymers; to further 'include', polymers can
be defined before clusters when in expert mode
- Changed bash script global loop variable names to all caps
20211029 - Added -lammps_error to control restart upon error
- Added -[no]error to resulting run shell scripts
- Added -[no]debug to resulting analyze, build, and run shell scripts
20211006 - Changed -phases interpretation: unused clusters are assigned to the first
empty phase; remaining empty phases cause an error
20210801 - Web publication
20210729 - Changed variable replacement order
20210723 - Added rudimentary math for ITEM MASSES
20210722 - Improved field location routines
20210721 - Changed the creation of mass in case of replicas; mass is not redefined
when already set under ITEM MASSES
20210718 - Fixed ITEM LAMMPS verbatim additions to lammps input script
- Added gyration to sample option for radii of gyration determination
through sampling by LAMMPS
20210710 - New version: 4.1
- Added -split to control partitioning of surface clusters
20210704 - Improved field locator
20210628 - Corrected behavior of expert and profile options
20210530 - New version: 4.0
- Retired .csv as a valid script extension; valid is only .esh
- Added ITEM INCLUDE to include separate parts of scripts
- Added ITEM WRITE to write out a line of text
- Added -location to prepend paths for various file locations
- Fixed usage of ~ in field_location path
20210527 - Added -system and -system_geometry options; the latter checks, if new
geometries are large enough to contain polymers from previous phases
(switched on by default)
20210521 - Fixed double write-out of LAMMPS input script footer
20210424 - Moved CMAP call to EMC .params
- Enriched placement of ITEM LAMMPS verbatim paragraphs
- Expanded -shake option to specify types, bonds, angles, and masses by
using type indicators
- 20210429 Updated ITEM ANALYSIS to correctly interpret script name
20210406 - Added -emc_progress to control progress indicators
20210328 - Changed internal ITEM VARIABLES representation
20210316 - Changed interpretation of -pair
20210224 - New version: 3.10.2
- Added -emc_exclude option to control exclusion of sections
- Added -emc_export option to control exported formats
20201223 - Adapted field locator to function properly under MSWindows using
Strawberry Perl
20201121 - Added bias to polymer options
20201029 - Added optional comment option to all ITEM statements, i.e.
- ITEM [COMMAND] [comment=[true|false]]
20200928 - Added normalization control to source fractions of replicas
- (see create_replicas())
20200921 - Improved cluster profile designation
20200915 - New version: 3.10.1
- Added polymeric group capabilities
- Sorted group connectivities
20200825 - Forced all variables to be lower case when reported in .params
20200821 - Added environment variable 'EMCROOT'
- Added option 'formal' to cluster import options
20200817 - Corrected InsightII import
20200804 - Added trim functionality for trimming terminal spaces
- Adapted behavior of lines with mixed comma and space separators
20200801 - New version: 3.9.7
20200630 - Corrected initial sizing of imported structures
- Introduced lprevious as variable for length of previous phase
20200615 - Corrected variable handling
20200602 - Improved variable handling in loops
- Altered -build_center to allow for setting of origin
20200518 - Added -insight option for writing InsightII CAR and MDF
20200511 - Added -pdb_expand option to allow for expanded format for PSF
20200428 - Added sorting of fields
- Added element targets for group connections
- Adapted sorting of field ids
20200407 - Generalized use of field_id
- Added unwrap and guess options to cluster import
20200219 - Changed behavior of -field option to include improved search
20200214 - Added -cutoff option to set a list of cut offs
- Added -ghost_cut option for setting LAMMPS ghost region size
20200131 - Corrected behavior of adding additional bonds when transferring
- DPD nonbonds to bonds
20200127 - Added check on number of clusters for polymer mass and length
normalization
20191119 - Changed behavior of non-occurring cluster from warning to error
20191118 - Added update_field() to update behavior of field options
20191006 - Added ITEM EMC as equivalent to ITEM VERBATIM
20190902 - Added -lammps_dlimit for controling nve/limit maximum distance
20190817 - Added -queue for general access to queue settings,
-queue_account to allow for queue accounting and -queue_user for
queue-specific user-defined commands
20190728 - Added -moves_cluster for controlling molecular distribution
- Added use of moves and types keywords in EMC build script
20190718 - Changed neighbor list to multi for DPD; added -nocite to lammps
20190715 - Retired -units=lj and introduced -inits=reduced instead
20190710 - Added -pdb for controlling PDB/PSF output
- Changed behavior of -lammps and -emc to exclude reset_flags()
20190701 - Reordering of phase build up, coupling field apply to clusters
20190622 - Improved variable replacement handling
- Added exclude as identifier for importing in ITEM CLUSTERS
- Improved ITEM VERBATIM option handling
- Added environment variable 'WORKDIR'
- Added option -workdir to set an alternate work directory
20190606 - Updated behavior of phase=-1 for ITEM VERBATIM
20190604 - Added -pdb_rank to allow for rank analysis for PDB output
20190521 - Added keyword 'all' to -phases option to indicate all clusters
- Refined phase splitting
20190511 - Changed replace.pl to add curly brackets around variable definitions
20190503 - Added phase=# and spot=# to 'ITEM VERBATIM' where # can be a number or the
word 'last', phase E [0,..,nphases], spot E [0,1,2]
20190501 - Improved behavior for additional nonbonded parameters using
- 'ITEM NONBONDS'
20190427 - Changed -pdb_compress default to true
20190424 - Changed behavior of -build_replace in subsequent run scripts
- Added value of option -seed to build.emc
- Added -field_dpd options
20190418 - Allowing for hash as comment in options
- Allowing for non-existing polymer definitions in expert mode
20190416 - Allowing for undefined clusters in expert mode when defining phase
contributors
- Cleaned up command line behavior for setting project name and main script
20190410 - Changed location interpretation of chemistry/stages dirs
- Added -niterations for control of build interations
- Consolodated build settings in $::EMC::Build
20190408 - Corrected parsing behavior of loop variables
- Added -pdb_compress option
20190318 - Altered behavior of ITEM VERBATIM 0 [0|1], which allows for usage of
verbatim before (mode 0) and after (mode 1) sizing old(ITEM VERBATIM 0
[0]) = new(ITEM VERBATIM 0 1)
- Added expert mode to interpretation of environment variables, such that
constants can be used in conjunction with loops
20190126 - Added :f[ield]=id option to group identifiers to force using a specific
field id for typing when using multiple fields
20190110 - Adapted treatment of CHARMM to include correct use of switching function
for both pair and pair14 (in dihedral) contributions
20181228 - Adapted interpretation of sample flags for analysis
- Added -- to all calls to perl to allow for arguments starting with a minus
sign (GNU convention: point where options stop)
20181218 - Corrected missing initial creation of chemistry directory
20181214 - Fixed issue assigning chunks for MSDs in LAMMPS input
- Added -field_nbonded to DPD field bonded inclusions
- Corrected the use of chunks for profiles and MSD
- Added average as choice for option -msd combined with new LAMMPS compute
msd/chunk/ave (derived from msd/chunk) and analysis routines
20181129 - Corrected behavior for additional user analysis scripts
20181116 - Added -field_format to control format in generated field when using 'ITEM
FIELD'
20181103 - Corrected inclusion of field in template
- Added -build_order to build clusters in order as provided by
-phases
- Migrated -center to -build_center
- Updated variable behavior to avoid incorrect interpretation when using
e.g. @A and @AA as loop variables
- Correction for field type colloid
20181029 - Corrected behavior for (re)starting packed jobs
20181027 - Corrected multiple jobs per node behavior for local queues
20181014 - Added end-to-end analysis
20181013 - Changed behavior for fields with possibly uncharged systems
20181010 - Allowing for project names with slash in name: last part will will be
project name; whole name will be script location
20181009 - Corrected inclusion of .params file during analysis
20181008 - Added -analyze_source to set the location source of the data directory
- Added -polymer_niters to control the number of iterations used to build
(branched) random polymers
20180930 - Added radius of gyration analysis
20180926 - Added possibility for adding optional cutoff and gamma to
- DPD nonbonds
20180925 - Added :w option to sequence interpretation to enforce equal width (usage:
e.g. s:2:10:2:w)
20180921 - Renamed -chemistry to -script and changed associated internal variables
- Reorganized global constants
20180919 - Expanded loop sequence interpretation to include previously defined loop
variables (e.g. @X refers to x)
- Added -lammps_pdamp and -lammps_tdamp for setting damping constants
20180901 - Corrected behavior for nonbonded wildcards
20180825 - Forced -emc_execute=false in environment mode
20180814 - Changed compute com/msd to msd/chunk
20180803 - Fixed inclusion of atomistic and united atom force fields
- Added -field_reduced to override reduced units defaults
20180801 - Added -skin and integrated -units into LAMMPS input script
20180718 - Changed behavior with respect to queue sizing for preset machines
20180716 - Changed behavior of -record to allow for more control of resulting PDB
20180710 - Moves option -depth to -emc_depth
20180708 - Added items ENVIRONMENT [project] (acts as OPTIONS; sets project when
supplied) and CHEMISTRY (identical to TEMPLATE)
20180705 - Improved run behavior upon LAMMPS restart
20180628 - Fixed write_emc_field_apply() to avoid empty types -> {}
20180626 - Added '(*' and '*)' at start of line as comment delimiters
20180622 - Fixed interpretation of pressure coupling for equal signs
20180620 - Fixed creation of test paths
20180612 - Improved functionality for using -build flag on run scripts
20180601 - Added sequence interpretation for test setup.sh
20180526 - Added -namd for creation of NAMD input
- Added -pdb_parameters for creation of NAMD .prm input
- Added multiple jobs per node using job packing
20180512 - Adapted designation of type variable for creation of type specific
profiles: moved to EMC .params file
20180503 - Corrected a directory issue with already existing builds while running emc
through build or run scripts
20180424 - Changed interpretation of 'copy' loop variable to allow for sequences
20180404 - Added interpretation of field type colloid including shear
- Renamed -replace_build to -build_replace
- Refined and streamlined behavior of -build_replace
20180402 - Fixed default behavior of set_list()
- Added -name_testdir for adding tests of chemistry paragraphs in
environment files; creates ./test/${name_testdir}/setup.sh
20180308 - Added -emc_run and -emc_traject for Monte Carlo equilibration after
building
20180224 - Added -analyze_data to control creation of exchange tar archive
- Added -analyze_replace to control replacement of existing results
20180217 - Rearranged order in run_emc() for both build and run scripts
- Changed focus behavior
20180215 - Added parameter evaluation for DPD forcefield definition
20180212 - Distinguished between build and run walltime in run scripts
20180207 - Added ITEM ANALYSIS for addition of user defined analysis
20180201 - Updated deformation of imported structures
20180131 - Changed mkdir to mkpath (File::Path) to create multi level directories
20180126 - Added -[no]emc and -[no]pdb flags to analysis scripts
- Adapted formatting of bash scripts
- Added deformation of imported structures
- Added project name to chemistry/stages for template writing
20180124 - Added interpretation of pdb_cut, pdb_unwrap, and pdb_vdw for analyze_last
in environment option paragraph
- Added control for execution of EMC for building during execution of build
and run scripts
20180123 - Added Berendsen barostat to LAMMPS input script for DPD
- Improved barostat coupling and direction options
- Loosened behavior of & line concatenation
20180120 - Added -emc_output for EMC output control
20180118 - Fixed issues with replacement while executing run script with
-norestart option
- Added help for command line options for build and run scripts
20180109 - Added flexible barostat options to reflect different coupling scenarios
20171203 - Updated various BASH script interpretational issues, including obtaining
th queueing system job ID for chaining LAMMPS jobs
20171127 - Added -weight for energetic weighting of force components as used by EMC
during structure building; replaces -grace
20171125 - Added treatment for imported structures
- Added -pdb_pbc and -pdb_unwrap flags to resp. control periodic boundary
conditions and unwrapping in PDBs
20171116 - Added -triclinic flag to force triclinic boxes in LAMMPS;
- Added (un)coupling of directions for LAMMPS NPT as extra keyword when
defining pressure
20171109 - Added sequences to loops when pairing variables
20171106 - Added keyword 'number' to import of clusters
20171031 - Added -crystal option for imported crystalline structures
20171029 - Added ITEM LAMMPS paragraph for verbatim additions to LAMMPS script
20171025 - Added triclinic treatment of box geometry
20171024 - Added -tighten to tighten simulation box around imports
20171018 - Added -expert to allow overrides of number checks for polymers
20171012 - Added -percolate option for crystalline InsightII structures
- Disabled NPT when invoking -pressure=false
20170927 - Fixed issue with recognizing loop variables when using colons
- Fixed issue with polymer fractions when using variables
- Corrected phase box sizing when building polymers
20170921 - Fixed issue with profiles
20170920 - Corrected error checking on existence of environment trial
- Fixed issue with usage of copy keyword in loops
- Fixed issue with reading field_name option
20170919 - Addition of references through ITEM REFERENCES
- Addition of parameters through ITEM PARAMETERS
20170917 - Consolidation of EMC, Lammps, and Parameter flags
- Application of strict Perl variable handling
- Addition of force field module for inclusion of full fields through ITEM
FIELD
- Fixed use of multiple entries for -field_name
20170914 - Set initial value of $::EMC::Lammps{trun_flag} to false
20170912 - Resolved issue with zero repeat units in polymers
20170830 - Added type 'density3d' to option and item profiles
- Added 'binsize' to options
20170823 - Excluded project name as possible profile name
- Added :h to LOOPS in environment to exclude variable from directory
structure
20170822 - Added -pdb_connect option
20170818 - Fixed issue with structures containing formatting signs in
- SMILES
20170816 - Added pressure profile for all atoms when selected
20170814 - Fixed issue with profile per type not using the correct types
20170812 - Moved write_emc_field_apply() from write_emc_clusters() to
write_emc_phase()
20170810 - Fixed issue with profile per type not being written
20170805 - Corrected output of number of polymers when using -number=true
20170728 - Fixed issue with multi-phase exclusion regions for DPD
20170726 - Added pressure profile sampling to LAMMPS script
20170725 - Added -thermo_multi to invoke multi thermo style in LAMMPS
20170721 - Added -replace_build flag for ignoring existing .data files during build
script execution; can alo be invoked by adding
-replace flag to ./build/.sh script
- Added use of -build flag in conjunction with ./run/.sh scripts, allowing
for invoking LAMMPS executing after EMC build; uses queueing system
chains
20170718 - Added -number for interpreting cluster fractions as number of molecules
- Fixed an issue with empty additional variables as offered to
write_emc_variables()
20170717 - Added -cut=repulsive for transfering purely repulsive potentials to LAMMPS
20170711 - Added EMC environment testing mode
20170701 - Improved behavior when importing structures
20170624 - Addition of -options export to GUI
20170622 - Excluded DPD nonbond wildcard entry when -auto=false
20170615 - Cleaned up structure interpretation
- Added :d or :double mode to environment loop variables
20170530 - Added project name to queue submission
20170221 - Added -analyze_last to control inclusion of last frame during analysis
20170517 - Added reserved word 'copy' to environment loop variables
20170514 - Added green-kubo as sample option
20170508 - Changed calling of -file for LAMMPS restart
20170506 - Changed from environment 'phase' to 'stage', maintaining backwards
compatibility
20170424 - Added pairwise exclude region when importing structures
- Added -region_epsilon and -region_sigma for defining exclusion regions
- Added -pdb_fixed and -pdb_rigid flags
20170412 - Added -direction flag for using different phase build directions
20170409 - Added -execute flag for executing EMC build script
20170406 - Added -pdb_cut, allowing for cutting bonds spanning the box
- Added 'import' to CLUSTERS paragraph as type to allow for importing
structures in either EMC or InsightII serving as surfaces etc.
20170326 - Added -nchains option, allowing for chains of simulations
- Included emc build phase in lammps run scripts
20170311 - Changed indexing of %::EMC::Field by adding @::EMC::Fields
20170223 - Added skip on existing .data during build
- Fixed thermo output in restart mode
20170220 - Added 'field_error' option
20170209 - Renamed options 'location', 'name' and 'type' to
- 'field_location', 'field_name' and 'field_type' respectively
- Added option 'name_scripts' to set analyze, build, and run names
simultaneously
20170208 - Adapted interpretation of multiple LOOP sections
- Added energy and volume time average paragraphs for LAMMPS input script
20170207 - Allowing only unique entries in LOOP variables
20170131 - Fixed issues with field designation
20170124 - Added shake option and adapted type interpretation
20170113 - Added build directory creation to environment setup
- Take chemistry file name as default for run names
20170106 - Added replacement of one nonbond entry with another
20161121 - Added loop pairing to pair variable with previous
20161114 - Corrected nl_ composition for polymers
20161031 - Added environment mode for generation of project directory structure and
parallel run scripts
20161026 - Added pressure and shear paragraphs to be reflected in lammps input file
20161025 - Added internal shake flag to allow for stable runs
20160922 - Added -hexadecimal
20160908 - Added -center, -depth, and -record
20160818 - Fixed chunk usage
- Added -dtthermo, -dtrestart, -trun, and -tequil
20160804 - Added all field flag options for angle, torsion, improper, and increment
(angle now has dual functionality)
20160720 - Added 'old', 'new', and year options for -lammps to set -chunk and
-communicate; set default to new LAMMPS versions
20160628 - Added ITEM OPTIONS for setting command line options in the chemistry file
20160624 - Added option -warn to allow for warning output control
20160620 - Fixed replica interpretation
- Added variable paragraph to chemistry file
20160615 - Added Born potential hooks
20160524 - Altered behavior of mixed use of space and tab separators
- Altered passing of numbers of clusters from EMC to LAMMPS by introducing
variables starting with 'nl_'
20160511 - Fixed replica addition with missing references.csv
20160422 - Adapted inclusion of unit mass for added replicas
20160321 - Added verbatim end operation possibility
- Incorporated variable changes as a result of invoking surfaces
20160315 - Added -momentum flag to allow for zeroing momentum in lammps
20160310 - Added -nparallel for surfaces
- Added BOND and ANGLE paragraph to chemistry file for definition of
specific bonds and angles
- Added -bond=type1,type1,k,l & -angle=type1,type2,type3,k,theta command
line options to allow for command line addition of specific bonds and
angles
20160222 - Added line extensions '&' and '\' to input
- Added surface incorporation to CLUSTERS
20160217 - Added increment warning flag to navigate missing increments
20160126 - Added block on mass and volume entry in chemistry file for atomistic force
field
20160120 - Generalized LAMMPS input script to be used for either equilibration or
restart
20160119 - Refined force field choice
20151130 - Added $::EMC::MD{restart} and $::EMC::Shear
20151127 - Added $::EMC::Lammps{prefix} for adding project prefix to output and
$::EMC::Lammps{chunk} for using chunk approach in profiles
20151123 - Broadened force field recognition (e.g. -field=dpd/general)
- Debugged interpretation of -charge=false for -field=dpd
20151117 - Added keyword VERBATIM to chemistry file interpretor for adding verbatim
EMC scripting to build file
20151111 - Changes in LAMMPS input script for DPD:
- Removed langevin thermostat
- Changed neigh_modify from 'delay 1 every 1' to 'delay 0 every 2'
- Reduced default charge cutoff from 4.0 to 3.0
20150925 - Corrected behavior when selecting mol fractions
20150801 - Added 'ITEM SHORTHAND' and 'ITEM COMMENTS' to chemistry file
20150714 - Added group[:group[:...]] and n[:w:w[:...]] to POLYMERS to allow for
statistical drawing of group identities
20150630 - Added id[:t] to identify forced terminator groups
20150610 - Added focus for molecules
20150528 - Added -communicate to cover change from communicate to comm_modify in
newest versions of LAMMPS
20150522 - Added correction for DPD interaction parameters based on reference volumes
and actual volumes
20150519 - Reworked chemistry.csv format to include polymers, using paragraph
keywords starting with 'ITEM'; legacy file format is still valid
20150511 - Added inclusion of extra clusters in LAMMPS input script when using the .
separator in SMILES
- Altered behavior of -emc, -lammps, and -params flags
- Added -replace flag
20150430 - Added disallowed cluster names
20150428 - Adapted mass interpretation for DPD implementations
20150424 - Corrected minor bugs for DPD implementations
20150416 - Added coulomb->pair for non-DPD force fields
20150408 - Added cross flag to lammps for DPD and MARTINI
20150316 - Added neighbor paragraph for DPD implementations
20150306 - Added refinements to accomodate DPD implementations
20150303 - Corrected entries for CHARMM and MARTINI implementations
20150216 - Added overwrite safeguards for created scripts
- Added density designation for each phase
20150211 - Added radius and grace adaptations for dpd force fields
- Debugged multiphase system setup
20150205 - Changed opls{aa, ua} to opls-{aa, ua}
- Added trappe force field options
20141222 - Repaired msd and profile flag operation
- Added extra comments to lammps input script
20141220 - Changed to using mass() and nsites() in EMC scripting
20141218 - Added atomistic interpretation of ntotal
- Added lbox determination in terms of mass density [g/cc]
20141129 - Addition of dpd_setup.pl routines
20141124 - Addition of referenced extra parameters
20141118 - Repaired appearance of density profiles in LAMMPS script
20141102 - Combined dpd_setup.pl and atom_setup.pl into emc_setup.pl
20141019 - Added checks for force field topology
20140730 - Added -seed flag to set initial random seed
- Updated use of charges
20140614 - Added multiple phases to command line by introducing a '+' sign as
demarcation
- Fixed issues upon absence of a reference file
20140327 - Changed to implement as DPD force field
- Added -angle and reference file for cut off and mass scaling
20120614 - Corrected mistakes in bond interpretation
- Added global setting of parameters to constant value
- Added number check on lammps density profiles
- Added lower bound on parameters
20120612 - Bug-fix phase determination in read_chemistry
- Added molecular volume read from chemistry column 5
- Added volume flag to allow for weighting by molecular volume
- Added extra flag for creating parameter copies
- Stream-lined fraction interpretations
20120503 - Addition of charge paragraphs
20120502 - Mass-related bug fix
20120419 - Bug-fix concerning density profile cluster order
- Alignment of pressure profile frequency with density profiles
- Inclusion of _chem and _parm wildcard suffixes
20120224 - Addition of build, assume, and frequency flags
20120210 - Addition of temperature to parameters
20120204 - Inception