History
v9.2 v9.3.1 v9.3.2 v9.3.3 v9.3.4 v9.3.5 v9.3.6 v9.3.7 v9.3.8 v9.3.9 v9.4.1 v9.4.2
v9.4.2
Date Description
------------------------------------------------------------------------------
20170601 - Change over to new version
- Added geometry() function to ./core/parse.c
- Added functionality to ClusterUnwrap(), reflecting different
unwrapping modes
- Added a new force field region/lj in ./core/types/region/lj.c for
simulating pairwise regions as used during builds around structures
- Added periodic option to ./script/translate
- Added ClusterCut() and ListCompare()
- Changed EMC script read to literal interpretation of variables
- Added environment mode for looping over variables in EMC setup
scripts, supporting high performance computing
- Added queue chain options to EMC setup
- Grouped options in EMC setup
20170614 - Added PDB read, using PDB and PSF
- Added group initialization based on group tags, allowing for
recognition of repeat units in polymers, when properly specified
- Improved EMC setup environment functionality
20170615 - Cleaned up structure interpretation in EMC setup
- Added :d or :double mode to environment loop variables
20170622 - Excluded DPD nonbond wildcard entry when -auto=false
20170624 - Addition of -options export to GUI
20170701 - Improved behavior when importing structures
20170711 - Added EMC environment testing mode
20170717 - Added -cut=repulsive for transfering purely repulsive
potentials to LAMMPS
- Repaired behavior of SDK potentials when ported to LAMMPS
20170718 - Added -number for interpreting cluster fractions as number of
molecules
- Fixed an issue with empty additional variables as offered to
emc_write_variables()
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
v9.4.1
Date Description
------------------------------------------------------------------------------
20160905 - Change over to new version
20161006 - Addition of typing by multiple fields as needed by charmm
- Moved storage of io function to ListCommonRead() and
ListCommonWrite()
- Added fields to simulation->constants to allow for field ids
- Generalized force field application routines for assorted fields
- Corrected wildcard recognition for torsions (e.g. CHARMM)
- Added fixed width for atom index in PDB file
- Added recording options during the build process
- Added general module template to ./core
- Added general list template to ./core/field
- Generalized ./core/field apply and parameters as template for use
with various force fields
20161105 - Generalized ./core/field rule as template for use with various
force fields
- Added ./core/field/list/{bond, cross, wildcard}
- Integrated bond recognition into FieldInit()
- Changed behavior insight->crystal flag by treating all crystal
connections in .mdf as regular connections
- Added ./core/{field,port/lammps,types}/colloid force field
- Fixed bug in ./core/moves/endbridge
- Addition of environment mode to emc_setup.pl to allow for
parameter studies using either LSF or PBS queueing systems
20161220 - Fixed OPLS-UA typing rules to correctly type PET
- Corrected wildcard behavior for angles
- Broadened PSF type to six characters
- Corrected behavior of ListCommonWrite()
- Addition of environment definitions to EMC manual
- Addition of environment shear setup example to EMC manual
- Corrected torsion transcription to multi harmonics for OPLS, TraPPE,
and GROMACS force fields
- Corrected OPLS-UA rules to reflect correct typing of PET
20161031 - Added environment mode for generation of project directory structure
and parallel run scripts to emc_setup.pl
20170103 - Fixed ScriptGroupsGroupAppend()
- Fixed behavior of reading literal constants (11BPN is not translated
to a number with value 11)
- Fixed usage of TIP models with OPLS
20170312 - Added type SHAKE capabilities to emc_setup.pl and emc
- Improved InsightII port
- Fixed interpretation of cff rules using allowed and disallowed tests
- Fixed issue with skipping of absent types for cff force fields
- Fixed issue with use of nclusters() and ntotal() in ./core/parse.c
- Fixed issue with absent atom names in PDB and PSF
- Swapped first two improper atoms in PSF for NAMD compatibility
- Checked for memory leaks
v9.3.9
Date Description
------------------------------------------------------------------------------
20150901 - Change over to new version
20151009 - Added terminator specification to polymer definition in
./core/script/clusters/polymer.c
- Added test for like polymer in _ClusterSites() for down hydrogen,
which is needed for grafted structures
- Added FieldRuleListOrder() to FieldRuleInterpret() to ensure
correct rule order during interpretation
- Added esters to OPLS-UA
20151211 - Repaired interconnected ring treatments in martini.pl
- Changed LAMMPS DPD defaults in emc_setup.pl
- Extended emc_setup.pl to allow for dendrimers
- Added dendrimer extension to polymer construction
- Corrected mass assignment of terminator groups during polymer
construction
- Created correct treatment of block and alternate copolymers
- Removed double entries when building additional clusters during
polymer construction (i.e. counterions etc. using *[A+]*.[B-])
- Corrected crash when building multiphase systems by resetting
sectors and images when reallocating sites
- Corrected LAMMPS CHARMM dihedral output, including parameter file
entries
20160118 - Added ./field/charmm/c36a including CGENFF
- Direct translate of CHARMM prot and cgenff files from src directory
- Added cgenff.define to allow for deviations from automatic translate
20160125 - Corrected bond sampling to use bonded instead of cluster lists
- Updated TraPPE-UA, OPLS-UA, and OPLS-AA force fields
- Improved charmm.pl mass recognition, topology file interpretation
- Debugged sampling capabilities by updating ./core/samples/{bond.c,
distance.c, gr.c, gyration.c}
- Added ListCommonIOGet() to ./core/{focus.c, region.c} to allow for
recursive use
- Updated ./port/lammps/charmm to reflect correct torsion treatment
- Changed ./core/script/traject to use put, get, and sample; changed
default of 'scale' to false
20160217 - Repaired interpretation of charmm/c36a/cgenff interpretation to
correctly type ring members
- Repaired typing of fluorides in opls/2015/opls-aa
- Added an increment flag to emc_setup.pl to bypass missing increments
in CFF force fields
- Switched to hexadecimal representation of residue field in PSF
- Improved ring recognition for structures consisting of
interconnected rings of different sizes
20160404 - Added FieldCopy() to ./script/crystal
- Resolved quote issues with string command line variables
- Adapted ./scripts/emc_setup.pl to include surfaces
- Changed ./core/script/{flag.c, retype.c} to exclude non-built sites
when ranges are defined
- Corrected auto angle interpretations of cff force fields
- Corrected behavior of repeated additions to chemistries, i.e.
charged polymer ([A-])10(.[B-])10 with 10 monomer units A and 10
counter ions B
- Added REPLICAS, NONBONDS, BONDS, and ANGLES paragraphs to
chemistry.csv file syntax
- Corrected sequence interpretation of source and destination in
./core/script/retype
- Added focus to ./core/script/retype
20160509 - Added script option to sample scripting command
- Added recognition of compressed files ending with .gz in get, put,
traject, lammps, pdb, and xyz scripting commands
- Refined ./core/script/retype to allow for retyping of non-build
clusters; corrected reading of retype->n
- Corrected script line count for files with both 0x0d and 0x0a at eol
- Adapted ClusterSites() to allow for proper head-tail crossing to
counteract cluster wrapping issues
- Made GroupsBuildClusterBased() more robust to allow for better
SMILES recognition
- Fixed a bug in ChemistryRings() by introducing
CHEMISTRY_RING_MINDEPTH to force proper ring recognition in case of
alternative SMILES
- Added types to charmm/c36/cgenff to account for polystyrene
20160704 - Fixed SMILES interpretation of E/Z isomers
- Fixed angle refinement Monte Carlo scheme in ./core/grow.c
- Fixed recognition of 'all' keyword for simulation->types->shake
- Fixed focus selection for parse functions nclusters(), ntotal(),
and mtotal()
- Added Born potential including force field typing and LAMMPS
parsing
- Adapted emc_setup.pl to correctly interpret neutralizing ions when
added to monomers used in polymers, thus fixing issues with profile
definitions for LAMMPS input scripts
- Adapted emc_setup.pl to allow for mixed use of tabs and spaces in
chemistry.csv
- Corrected shift interpretation in ./core/types/charmm/pair.c;
potentials are shifted when the repulsive is selected or
inner >= cutoff and shift is set to true
- Tested ensemble correctness by a rudimentary interpretation
- Fixed a SEGV issue while copying in ./core/script/clusters/groups.c
- Fixed missing terminator for alternate and block (co)polymers
- Added options interpretation to emc_setup.pl chemistry file
- Adapted emc_setup.pl to allow for use as an interpreter
- Generalized interpretation of DATA_NCOEFS for force field porting
- Fixed porting of DPD torsions to LAMMPS
20160819 - Fixed FieldRuleIndexCopy() (crystal issue)
- Fixed behavior of SiteConnectClean()
- Updated manual to include emc_setup.pl examples
- Fixed LAMMPS input script generated by emc_setup.pl for -lammps=new
- Corrected opls/2012/opls-ua rules for imides and esters
- Added charmm/c36a/cgenff missing bonded contributions for (poly)
propylene oxide
20160905 - Added fixed width for atom index in PDB file
20161011 - Corrected swapped error and debug in script->field
20161220 - Corrected torsion transcription to multi harmonics for OPLS, TraPPE,
and GROMACS force fields
- Updated OPLS-UA parameters to correctly type PET
v9.3.8
Date Description
------------------------------------------------------------------------------
20141008 - Change over to new version
- Corrected automated force field recognition for ./core/script/pdb.c
and ./core/script/lammps.c
- Corrected ./core/field/rule.c to parse wildcard recognition to rule
testing; needed for correct recognition of charged substituents
- Updated ./core/script/clusters/polymer.c and ./core/field/apply/*
to reflect multiple types and partial charges at branch points and
directly neighboring sites by adapting group representations
20141019 - Added SDK (Shinoda-DeVane-Klein) force field plugs for typing and
generation of initial configurations for available ports
- Added and tested an SDK example to ./examples/setup/atom/sdk
20141107 - Fixed a bug in ./scripts/martini.pl related to creating correct
SMILES for templates that contain rings
- Disallowed 2-membered rings by adapting ChemistryRings() in
./core/chemistry/ring.c
- Added -msd flag to ./scripts/atom_setup.pl and
./scripts/dpd_setup.pl to add MSD calculation to resulting LAMMPS
input scripts
- Added -profile flag to ./scripts/atom_setup.pl to add density
profile calculation to result LAMMPS input scripts
- Debugged FieldApplyIncrements() in ./core/field/apply/increments.c
to improve charge assignments at group sites next to branch sites
20141214 - Adapted iteration error message in ./core/script/clusters/polymer.c
to read "exceeded niterations for polymer ..."
20150102 - Added mass() and nsites() functions to ./core/parse.c for use in
EMC scripts
- Added ./scrips/emc_setup.pl as replacement for atom_setup.pl and
dpd_setup.pl
- Updated PCFF force field files
- Updated ./field/opls/2012/{opls.pl, oplsaa.define}
- Passed functionality test with ./examples/field/opls/aa/{octane.emc,
ethanol.emc, acetic_acid.emc, benzene.emc, ethyl_benzoate.emc}
- Updated FieldRuleListSort() to include new recursive rule_order()
during sort to reflect correct rule ordering (wildcards last)
- Added ./core/samples/{list.hh, script.hh} templates to generalize
sampling routines
- Added template functionality to ./core/samples/cavity.c
- Added ./core/samples/{gr.c, gyration.c} for radial distribution and
radius of gyration sampling
- Debugged ./core/samples/cavity.c to include family->active flag
for activating energy calculations;
- Reworked ./core/script/sample.c to include sampling template
functionality
- Passed functionality test with ./examples/sample/cavity/build.emc
- Passed functionality test with ./examples/sample/gyration/sample.emc
- Passed valgrind test for new sampling functionalities
20150110 - Updated version including documentation
20150205 - Moved ./field/opls/2012/opls.pl to ./scripts/opls.pl
- Updated and added opls-aa force field definitions
- Moved ./field/opls/2012/{oplsaa, oplsua} to
./field/opls/2012/{opls-aa, opls-ua}
- Updated opls examples and ./script/emc_setup.pl to reflect change
- Added alcohols based on sugars to CHARMM force field
- Added ./field/trappe/2014/trappe-ua.define
20150308 - Updated ./core/type.hh to correct initialization order in TypeInit()
by placing TypeXRefInit() at end
- Deleted coefficients in general porting of data in
./core/types/charmm/torsion.c due to variable memory use for coeffs
- Removed memory leaks associated with the CHARMM force field
- Cleaned up sulfate and phosphate recognition in SMILES to allow for
RO:S(:O)(:O)(:O) == ROS(=O)(=O)[O-] and ROP(:O)(:O)OR ==
ROP(=O)([O-])OR (analoguous to R(:O)(:O) == R(=O)[O-])
- Updated BASF force field to represent sulphates and phosphates
correctly
- Added basf as cff field to emc_setup.pl (-field=basf)
- Corrected multiphase interpretation by emc_setup.pl
- Corrected ./scripts/charmm.pl to reflect all aromatic bonds as
partial
- Adapted ./field/charmmm/c32b1/all27_prot_lipid.define to reflect
sulfates correctly
- Passed ./examples/field/charmm/amino_acids/run.sh test
- Passed ./examples/examples/multiphase/surfactant/setup.sh test
- Started addition of Insight port for reading .car and .mdf
20150324 - Streamlined SMILES interpretation by altering site layout for
rings and repetitions through "()n"
- Added link identifier to ./core/chemistry/ring.h
- Altered bit representation for rings to allow for more than 64 rings
per group: bits are reused when rings do not overlap
- Debugged ./core/chemistry/{bond, link, ring, smiles} for correctly
representing graphenes
- Tested smiles with ./examples/test/smiles/build.emc: passed cluster
test, which uses ChemistryFromList() (needed for import ports, e.g.
./core/port/insight.c)
- Created new recursive ClusterBuild() to create correct cluster
extremes and ring linkage recognition
- Added a swapped array to avoid double swapping in SitesSort()
- Adapted ./core/port/insight.c to reflect new ClusterBuild()
- Added ./core/group/build.c and ./core/groups/build.c; the latter
switches to single-site groups when no suitable cluster-based
group can be found
- Passed ~/work/emc/port/insight/test/{6-propyl-dodecane, benzene,
branched, dodecane, ethO, gypsum, octane, rings, talc,
triphenylene} tests
20150511 - Correction of port/insight.c to box angle interpretion
- Addition of grow->include to allow for a grow->exclude counterpart
- Correction to GroupInit() to correctly interpret counter ions by
debugging group->additions interpretation
- Addition of atomistic field to insight port to allow for import of
united atom configurations
- Debugged ./core/script/crystal.c to repair box geometry errors
- Expanded ./core/script/translate.c selection options
20150520 - Reworked ./scripts/emc_setup.pl to include polymer definitions
- Modified ./core/script/clusters/polymer.c to reflect new
emc_setup.pl functionalities
- Added description of new functionality to manual
- Added a polymer example to ./examples/setup/polymer/
20150603 - Changed ./core/script/groups/polymer.c such, that 'head' and 'tail'
are displayed in the output when using head/tail identifiers
- Corrected OPLS-AA to include all hydrocarbon parameters for SP3
carbons (ct) next to aromatic carbons (ca) to deal with styrenics
- Repaired OPLS-UA to correctly interpret acrylics
- Added -communicate to ./scripts/emc_setup.pl to cover change from
communicate to comm_modify keyword in newest versions of LAMMPS
- Corrected behavior of selections in ./core/focus.c by increasing
format->target before calling ListCommonRead()
20150727 - Corrected SMILES ring interpretation to correctly reflect POSS
- Added zeolites to TraPPE force field
- Repaired crash in OPLS-AA ethanol/water typing
- Repaired moves/reptate.c to include targets in separate list
- Added fractional extensions for polymers in emc_setup.pl (needed for
multi-monomer polymers)
- Repaired reading field files through FieldRead() by debugging
FormatCount(), thus correctly counting the number of elements
- Added functionality to ./core/script/clusters/polymer.c to
include fractional multi-monomer polymers
20150805 - Published version, which includes tutorial examples for the
LAMMPS workshop
20150813 - Published version, which includes alterations to allow for use under
Windows
- Small changes to emc_setup.pl to avoid inclusion of carriage
returns in resulting build.emc files
v9.3.7
Date Description
------------------------------------------------------------------------------
20131106 - Change over to new version
- First version of CHARMM available
- Changes to rule interpretations needed for CHARMM support
- Addition of debug flag to field scripting command
20131206 - Fixed problem with aromatic rings being part of branches by adapting
looped sites in ChemistryRingRecurse() to SITE_NCONNECTS and
switching to reverse loop in ChemistryNConnects() (20131113)
- Added EZ isomers to chemistry.c (standard SMILES) and grow.c
(20131201)
20140103 - Enhanced ./core/script/clusters/polymer.c to construct complex
monomer connectivity correctly (iterative loop for filtering out
failed sequences)
- Added pair15 to types/table to represent Kremer coarse-grained
polystyrene
- Adapted port/lammps to facilitate exporting types/table, including
pair15 in bond representations in .data and .params and exporting
all tables to .table output
20140111 - Added dendrimer interpretation to ./core/script/groups/polymer.c
for creating dendritic networks
20140203 - Added detection of alternate mass types for group ends with multiple
branch points
- Should add a xref table on branches for which connection corresponds
to which connected group (needed for types transcription)
- Forced shift for repulsive type option to avoid compact builds
- Added shift for all pair types (including spline-based types)
- Added target to ./core/moves/endbridge.c to preserve chemical
topology integrity
- Version sent to MIT
20140328 - Fixed problem with aromatic ring detection when using Kekule
representation in SMILES
- Added auto equivalence rule to BASF force field for c3az
- Fixed size and copy of element in ./core/mass.c
- Added target to ./core/script/cut.c and ./core/script/remove.c to
preserve chemical topology integrity
- Added an adaptive roots.nmesh to SplineInverseRec() in
./core/spline.c to accomodate for inverses of soft angle terms
- Fixed bug in ./core/variables.c: updated dest->max_var in all
occurrences of dest->var reallocation
- Fixed bug in SystemsCount(): added a boundary to
++ientry[isystem-system][isite->mass] as a result of undefined site
masses resulting from using templates in ./core/script/clusters
definitions
- Fixed bug in ScriptBuildSelect(): cleaned up skip when connected
to include a test on deleted and build site flags; continuation
commences, allowing for the site to be retried at a later occassion
- Added improper option to ScriptField()
- Added improper flag and 'empty' constant to ./core/field/flag
- Rewrote ./core/field force fields to interpret improper flag and
'empty' option
- CFF force field always operates as if 'error' option is set for
angle, torsion, and improper flags
- Added partial wildcards to bond interpretation by ./core/field/opls
- Moved global operator functions in ./core/list/common to list_common
structure
- Added ./core/script/groups/delete to delete a specific group site
- Added mass and nonbond wildcard interpretation to ./core/field
- Added ./core/field/dpd to allow for a coarse-grained tabulation
of DPD parameters
- Added c* auto interpretation of bonded ct to ./scripts/opls.pl for
OPLSUA
- Added ions to ./field/opls/2012/oplsua
- Added CHARMM to LAMMPS port in ./core/port/lammps/charmm.c
- Added pcff field to ./field/pcff -> still needs rule fine tuning
- Debugged polymer build in ./core/script/clusters/polymer.c
- Added error check in ChemistryRings() (./core/chemistry/ring.c)
- Made name interpretation in ./core/script/field.c consistent
to be {parameters, topology} for all force fields
20140528 - Added cff field recognition to ./core/script/field.c in case
order of names is reversed
- Added active flag to all type families
- Tightened up wildcard recognition during application of force
fields through ./core/field/*/apply.c
- Added TypesDestruct() to FieldApply() to erase existing types
- Added 'auto' option to port forcefield flag, supported by
ScriptPDB() and ScriptLammps() through TypesFamiliesDetect()
- Fixed problem with angle_style in ./core/port/lammps/dpd.c
- Added rule to OPLS-UA topology to satisfy polypropyleneoxide
- Added backslash interpretation to ./core/format.c and
./core/variable.c to allow for = characters in type constants in
input script
20140616 - Fixed PortLammpsCharmmBondsPut() to output correct types for bonded
paragraphs
- Added multi-phase interpretation to ./scripts/dpd_setup.pl
- Tightened command line molecule interpretation for
./scripts/dpd_setup.pl
- Updated ./scripts/dpd_setup.pl to correctly interpret cut off and
mass adaptations
- Fixed E/Z interpretation in ./core/{chemistry.c, variable.c, grow.c}
- Added chain length delimiters to ./core/moves/{endbridge.c,
reptate.c}
20140923 - Adapted ./core/field/cff such, that spurreous extra types in rules
are neglected
- Corrected FieldRuleFlagCompare() for honoring both source and
destination 'any' bonds
- Corrected ./core/field/dpd/parameters.c to exclude transcription of
'X' types to '*' types
- Removed erroneous double variable evaluation from script
interpretation
- Corrected conversion of literal variable names containing '"' to
increase name length by 1 for each occurence
- Corrected script variable interpretation to allow for correct
sequence interpretation by adding a format->transfer flag in
conjunction with adaptation of VariableRead()
- Corrected interpretation of triple bonds, avoiding a '#' being seen
as a comment
- Corrected ./scripts/insight2lammps.pl to correctly represent
molecule numbers as stated in .car/.mdf
- Updated ./script/dpdsetup.pl to use force field files for parameter
interpretation in light of creating a data bank
v9.3.6
Date Description
------------------------------------------------------------------------------
20130504 - Change over to new version
- Improved InverseTorsionDefine() to reflect correct 1-4 distance
- Update of ./scripts/atom_setup.pl
- Added ./core/system_flag.c to include control over geometry mapping
and charge requirements
- Added group->charges flag to reflect handling of partial charge
assignment for SMILES sites
- Added CHARMM typing in ./core/field/charmm
- Added ./scripts/charmm.pl for converting CHARMM .prm and .rtf format
into EMC .prm and .top format
- Adapted ./core/types/charmm/urray.h and ./core/types/bond.hh to
reflect three-site dependence of urray contribution
- Reworked ./core/command_line.c by deleting unnecessary options and
including better command line variable definitions
- Inclusion of $arg# as internal variable, where # E [0, 1, ...] to
capture command line arguments
20130601 - Added a catch for non-defined parameters in ./core/type.hh
TypeExtreme()
- Updated group recognition and LAMMPS import routines
20130629 - Added martini force field (types, field, port)
- Streamlined porting routines
- Fixed internal issues for torsions with delta != 0
20130704 - Fixed issues with OPLS bond and angle parameter interpretations
- Fixed issues with CHARMM bonded parameter interpretations
- Corrected CHARMM and OPLS LAMMPS port
- Adjusted manual to reflect force field representation as given in
literature
- Added keywords 'head' and 'tail' to scripting group interpretation
20130715 - Corrected index interpretation for cyclic SMILES in
./core/chemistry.c, i.e. indices can be reused once a loop has
been closed
- Corrected ring interpretation to correctly assign ring bits as
needed by ./core/grow.c
- Corrected mistake in interpretation of type->nbonded (use minimum
instead of maximum)
- Corrected problems with importing LAMMPS files with multiple use of
same bonded coefficients, i.e. when two bonds each containing
different mass types use the same LAMMPS bond type (should result
in addition of new bond type)
20130809 - Added error upon application of field without defining it first
- Cleaned up memory assignment during mixing rule application
- Fixed bug when reloading field by adding type data merge
capabilities upon reading parameters
- Corrected behavior of 'variables' scripting command
- Fixed bug for pair calculations of undefined but activated force
fields by adding a return when xref == NULL
- Fixed bug in ./core/chemistry.c when using repeating sequences with
parenthesis, e.g. "(NCC(=O))3"; corrected connectivity (not to last)
- Cleaned up alpha carbon representations in PDB output
20130826 - Fixed issues with the cff force field implementation for bond_angle,
end_bond_torsion, angle_torsion, and angle-angle energies by
aligning EMC, LAMMPS and Materials Studio results
20130921 - Created .vmd output when exporting PDB format, thus transfering EMC
radii to a VMD readable TCL format
- Adapted growth of statistical copolymers such, that the number of
contributing groups entered through nrepeat are distributed
correctly over the copolymer (./core/script/clusters/polymer.c)
- Added the option of repeat units doubling as both repeat and
terminator for coarse-grained simulations (./core/group.c and
./core/script/groups/group.c)
- Increased the maximum number of terminators to 32
- Upgraded MARTINI .prm format to be more self-consistent
v9.3.5
Date Description
------------------------------------------------------------------------------
20121112 - Adapted charge on sites in groups; involved corrections to
./core/field/apply/increments.c and ./core/script/groups/group.c
- Corrected site flag issues in ./core/cluster.c stemming from
junction issues by rewriting ClusterChange()
- Version shipped to MIT
20121117 - Increased charge limit in SystemsCheck()
- Repaired recognition of deprotonated acids
- Improved determination of inverse angles in InverseAngleInit()
20121211 - Intermediate version for archiving purposes only
20121219 - Inclusion of OPLS force field typing: changes to core/types,
core/field, and core/port
- Creation of internal EMC .prm format for OPLS interpretation
- Adaptation of types->atomistic indicator to include none, united,
and full as keywords
- Creation of FieldApplyGroupsCharge() to generalize charge
assignments
- Addition of templates to field and .prm format
- Inclusion of templates to group and cluster assignments in scripting
20130210 - Correction of SitesBackbone() to exclude torsion contributions in
triangular structures
- Inclusion of ./scripts/martini.pl to translate GROMACS .itp format
to EMC .prm format; see field scripting in EMC manual
- Addition of ./core/samples/cavity.c: working prototype
- Addition of ./core/solver modules broyden.c, newton.c, and
line_search.c to be used in conjunction with
./core/samples/cavity.c: still in testing phase
20130310 - ./core/solver module tested for both broyden and newton with
line_search.c
- ./core/sample/cavity.c delivers correct cavities for fcc and bcc
- Both stable and instable cavities are identified
- Addition of sampling capabilities to ./core/script/traject.c
- Addition of ./core/script/sample command with cavity subcommand
- Addition of ./core/script/export command with profile and sample
subcommands; used for exporting analysis results in both .m and .csv
formats
20130316 - Addition of SMILES functionality to allow for repetition of
chemical sequences
- Updated documentation to reflect cavity, export, sample, SMILES,
and traject changes
- Addition of $root constant to indicate the EMC root directory
20130320 - Added SplineMoment() to ./core/spline.c
- Added pair14 to struct types_functions in ./core/types/registry.h
- Changed TypeTypesRegistry() in ./core/type.hh to include pair14
functions
- Activated TYPE_INVERSE in ./core/types/charmm/pair14.c and
./core/types/opls/pair14.c
- Updated InverseTorsion() in ./core/types/inverse/torsion.c to
include pair14 interactions
v9.3.4
Date Description
------------------------------------------------------------------------------
20111204 - Updated and checked examples
- Updated manual (still in progress)
- Updated standard and multi stencil implementation
- Corrected coarse/lj disparate size interactions
20120611 - Repaired issues related to underestimating junction lists in
./core/cluster.c
- Updated bonded interaction
- Rewrote ForceBondedLists() and dependent functions
- Deleted all redundant representations from ./core/force/bonded.c
- Corrected TypeTrigToPow() to reflect correct derivatives; corrected
./core/types/cff/torsion.c, ./core/types/charmm/torsion.c, and
./core/types/standard/torsion.c accordingly
- ./core/moves/diffuse.c needs to be revisted (double bonds etc.
appear when checking ForceBondedIntegrity())
- Added recognition of a leading "~" as the user's home directory in
f_open() in ./core/format.c.
- multi stencil implementation has unresolved issues
20120715 - Corrected line reporting for errors by adapting read and write
routines in ./core/script.c, ./core/variables.c and
./core/variable.c
- Corrected ClusterUnwrap()
- Corrected ./core/port/lammps/dpd.c to reflect charge parameters
correctly
- Added Deem rebridging; correct porting is yet inconclusive
20120731 - Version for Juropa
20120808 - Added 'name' to ./core/build/select.c to capture intermediate state
- Added 'mode' to ./core/region.c to reflect hard and soft regions for
use with ./core/grow.c (hard: full exclusion; soft: exclusion for
first cluster site only)
- Perfected ./core/grow.c for growing of atomistic representations
- Monte Carlo relaxation of angles and torsions with high tension
- Random pick of first backbone site for cluster off-backbone torsion
insertion
- Tested atomistic builds with polyethylene, dimethoxyethane,
polyethyleneoxide, and benzene at liquid densities (see
./examples/field)
20120826 - Corrected pair cutoff implementation in field/apply
- Corrected improper calculations to represent correct lists for
single site force calculations in force/bonded; tested with
acrylic acid and benzyl cyclohexane
- Corrected torsional picks to 1) first site on backbone, and 2) sub-
sequent sites based on non-backbone site 4
- Application of torsion relaxation MC algorithm for distinct
cases only
- Made changes to ./core/cluster.c to reflect correct execution of
branched semi-crystalline polyethylene problems
20121102 - Adapted grow.c to include tetraeder treatment of side connections
in GrowSideConnect(), needed for atomistic treatment
- Adaptation of migrate.c to reflect tetraeder treatment
- Cleaning up of field.c and dependents using memcheck
- version increase to v9.3.5 to align with MIT
v9.3.3 Correct force field typing, multi-threading, working builder
Date Description
------------------------------------------------------------------------------
20110227 - Working version without multi-threading
- Recursive bonded interaction force calc without list optimization
20110313 - Working version with multi-threading
- Optimized bonded interactions -> ./core/force/bonded.c
- Bonded calculations completely outside threads
20110315 - Intermediate version
20110326 - Intermediate version (partial bonded in threads)
20110327 - Working version with optimized multi-threading
- Optimization by partial bonded calculations in threads
- Cleaned up thread representation (through simulation->threads only)
20110403 - Cleaned up small bugs
- Uses #include "core/header.h" in all header files
20110408 - Replaced #include "core/header.h" by needed module header files in
all header files
v9.3.2 Start addition of force field typing
Date Description
------------------------------------------------------------------------------
20100510 - Addition of rules
20100524 - Addition of field, working rule import
- Fixed reading literal constants
v9.3.1 Addition of build principle
v9.2
Date Description
------------------------------------------------------------------------------
20081128 - Working sector and link neighbor lists, list does not function
- Changing storage to allow for list neighbor list
20081130 - Working sector and link neighbor lists, list does not function
- Generalized pair functions, Ewald not adapted
20081202 - Working sector and link neighbor lists, list does not function
- Generalized pair functions, Ewald not adapted
- Changed verlet to allow for uncoupled lists
20090312 - Working sector, link, list, and pair neighbor lists
- Pre-release version