Merge pull request #24 from kevinshen56714/kshen/update-to-2024-version

Update to the 2024 version
kevinshen56714 · Jul 28, 2024 · 8f7ba8a · 8f7ba8a
2 parents 05ff325 + 4cb3751
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diff --git a/pyemc/emc/HISTORY b/pyemc/emc/HISTORY
@@ -159,6 +159,46 @@ Date     Description
 	 - Changed OPLS mixing rules from arithmetic to geometric according to
 	   Jorgensen et al., J. Am. Chem. Soc. 1996, 118, 11225
 20230801 - Web publication
+20230919 - Added port->links to accommodate identical atom designations in
+	   imported molecules by PortInsightMDFGet()
+	 - Introduction of emc.pl, a modular version of emc_setup.pl
+20231006 - Fixed field typing issues for connective groups, e.g. in polymers
+	 - Fixed merging of clusters when using crystal command
+	 - Cleaned up memory usage
+20240224 - Fixed numerical stability issue in GrowSideConnect()
+	 - Fixed compression for use of ".gz" in name for scripting export
+	   command
+	 - Added selection options for surface grafting
+	 - Successfully passed valgrind test
+	 - Fixed issues with increment designation for polymers
+	 - Disallowed application of non-group field to groups with field
+	   definitions
+	 - Alteration of TRAPPE-UA acid parameters using J. Phys. Chem. B 2004,
+	   108, 14130-14136
+20240428 - Added published COMPASS force field in ./field/compass
+	 - Fixed assigment of nsites in ring
+	 - Added capture upon writing of empty fields
+	 - Updated treatment of CMAP to align with LAMMPS 2023 and higher
+	 - Adapted group polymers to include monomers and dimers in polymer
+	   definition
+	 - Introduced lone pair representation
+20240703 - Fixed a memory leak when applying fields
+	 - Fixed EMC setup control settings for field_bond, field_angle,
+	   field_torsion, and field_improper
+	 - Added force field wildcard recognition for mass entries
+	 - Added field alteration to emc.pl by means of ITEM FIELD
+	 - Updated the use of CHARMM CMAP files for LAMMPS
+	 - Improved exported InsightII files
+	 - Various additions to CHARMM CGENFF (see templates in cgenff.top)
+	 - Added EMC setup polymer keyword 'sequence' as synonym for 'block'
+	 - Addition of lone pairs for use with benzene and related structures
+	   for CHARMM CGENFF
+	 - Added the use of force field templates as EMC Setup references
+	   in groups and clusters
+	 - Fixed issues with ring recognition
+	 - Fixed double occurrence of hydrogen atom names in PDB/PSF for e.g.
+	   alcohols
+20240801 - Web publication
 
 
 v9.4.3

diff --git a/pyemc/emc/bin/emc_linux_aarch64 b/pyemc/emc/bin/emc_linux_aarch64
diff --git a/pyemc/emc/bin/emc_linux_x86_64 b/pyemc/emc/bin/emc_linux_x86_64
diff --git a/pyemc/emc/bin/emc_linux_x86_64.fc15 b/pyemc/emc/bin/emc_linux_x86_64.fc15
diff --git a/pyemc/emc/bin/emc_macos b/pyemc/emc/bin/emc_macos
diff --git a/pyemc/emc/bin/emc_win32.exe b/pyemc/emc/bin/emc_win32.exe
diff --git a/pyemc/emc/docs/emc.pdf b/pyemc/emc/docs/emc.pdf
diff --git a/pyemc/emc/examples/setup/chemistry/bulk/chemistry.esh b/pyemc/emc/examples/setup/chemistry/bulk/chemistry.esh
diff --git a/pyemc/emc/examples/setup/chemistry/bulk/setup.esh b/pyemc/emc/examples/setup/chemistry/bulk/setup.esh
@@ -1,19 +1,19 @@
-#!/usr/bin/env emc_setup.pl
+#!/usr/bin/env emc.pl
 #
 #    file:	bulk.esh
 #    author:	Pieter J. in 't Veld
 #    date:	July 4, 2016
-#    purpose:	Chemical input for emc_setup.pl
+#    purpose:	Chemical input for emc.pl
 #
 #    notes:
 #    	- Create a simulation with water, alcohol, salt and a sugar
 #    	- Alternative to chemistry.esh file, containing an OPTIONS section,
-#    	  to be used with emc_setup.pl v1.5 and up
+#    	  to be used with emc.pl v1.5 and up
 #    	- Allowed separators are commas and tabs, which can be used
 #    	  interchangebly
 #	- Call with
 #
-#		emc_setup.pl bulk
+#		emc.pl bulk
 #
 #	  or (for MacOS or Linux)
 #

diff --git a/pyemc/emc/examples/setup/chemistry/bulk/setup.sh b/pyemc/emc/examples/setup/chemistry/bulk/setup.sh
diff --git a/pyemc/emc/examples/setup/chemistry/field/charmm/chemistry.esh b/pyemc/emc/examples/setup/chemistry/field/charmm/chemistry.esh
@@ -3,7 +3,7 @@
 #    file:	chemistry.esh
 #    author:	Pieter J. in 't Veld
 #    date:	March 18, 2015
-#    purpose:	Chemical input for emc_setup.pl
+#    purpose:	Chemical input for emc.pl
 #
 #    notes:
 #	- Create a simulation with 80% m/m water and 20% m/m ethanol

diff --git a/pyemc/emc/examples/setup/chemistry/field/charmm/setup.sh b/pyemc/emc/examples/setup/chemistry/field/charmm/setup.sh
@@ -16,7 +16,7 @@
 # usage with vmd after build: vmd -e solution.vmd
 #
 
-  emc_setup.pl \
+  emc.pl \
     -ntotal=1000 -field=charmm \
     -replace solution $@;
 

diff --git a/pyemc/emc/examples/setup/chemistry/field/charmm/solution.esh b/pyemc/emc/examples/setup/chemistry/field/charmm/solution.esh
@@ -1,19 +1,19 @@
-#!/usr/bin/env emc_setup.pl
+#!/usr/bin/env emc.pl
 #
 #    file:	solution.esh
 #    author:	Pieter J. in 't Veld
 #    date:	August 15, 2016
-#    purpose:	Chemical input for emc_setup.pl
+#    purpose:	Chemical input for emc.pl
 #
 #    notes:
 #    	- Create a simulation with 80% m/m water and 20% m/m alcohol
 #    	- Alternative to chemistry.esh file, containing an OPTIONS section,
-#    	  to be used with emc_setup.pl v1.5 and up
+#    	  to be used with emc.pl v1.5 and up
 #    	- Allowed separators are commas and tabs, which can be used
 #    	  interchangebly
 #	- Call with
 #
-#		emc_setup.pl solution
+#		emc.pl solution
 #
 #	  or (for MacOS or Linux)
 #

diff --git a/pyemc/emc/examples/setup/chemistry/field/dpd/setup.sh b/pyemc/emc/examples/setup/chemistry/field/dpd/setup.sh
@@ -21,7 +21,7 @@
 # usage with vmd after build: vmd -e dpd.vmd
 #
 
-  emc_setup.pl \
+  emc.pl \
     -field=dpd -mass -replace  \
     -profile -build_dir=. -rtype=WAT8 dpd nylon + branch + water
 
diff --git a/pyemc/emc/examples/setup/chemistry/field/generate/build.emc b/pyemc/emc/examples/setup/chemistry/field/generate/build.emc
@@ -1,6 +1,6 @@
 (* EMC: Script *)
 
-(* Created by emc_setup.pl v3.6.0, July 8, 2018
+(* Created by emc.pl v3.6.0, July 8, 2018
    on Sun Jul  8 12:15:11 EDT 2018 *)
 
 (* define variables *)

diff --git a/pyemc/emc/examples/setup/chemistry/field/generate/field.esh b/pyemc/emc/examples/setup/chemistry/field/generate/field.esh
@@ -1,4 +1,4 @@
-#!/usr/bin/env emc_setup.pl
+#!/usr/bin/env emc.pl
 #
 #  script:	field.esh
 #  author:	Pieter J. in 't Veld

diff --git a/pyemc/emc/examples/setup/chemistry/field/generate/field.in b/pyemc/emc/examples/setup/chemistry/field/generate/field.in
@@ -1,5 +1,5 @@
 # LAMMPS input script for standardized atomistic simulations
-# Created by emc_setup.pl v3.6.0, July 8, 2018 as part of EMC
+# Created by emc.pl v3.6.0, July 8, 2018 as part of EMC
 # on Sun Jul  8 12:15:11 EDT 2018
 
 # Variable definitions

diff --git a/pyemc/emc/examples/setup/chemistry/field/generate/field.prm b/pyemc/emc/examples/setup/chemistry/field/generate/field.prm
@@ -1,6 +1,6 @@
 #
 #  STANDARD interaction parameters 
-#  converted by emc_setup.pl v3.6.0, July 8, 2018 by Pieter J. in 't Veld
+#  converted by emc.pl v3.6.0, July 8, 2018 by Pieter J. in 't Veld
 #  to be used in conjuction with EMC v9.4.3 or higher
 #
 

diff --git a/pyemc/emc/examples/setup/chemistry/field/lj/field.esh b/pyemc/emc/examples/setup/chemistry/field/lj/field.esh
@@ -1,4 +1,4 @@
-#!/usr/bin/env emc_setup.pl
+#!/usr/bin/env emc.pl
 
 ITEM	OPTIONS