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1776 Commits

Author SHA1 Message Date
Axel Kohlmeyer c78d4eab36
update standard examples for new style names 2021-07-21 22:52:43 -04:00
Axel Kohlmeyer f8f4af471f
general rename of files, styles, and keywords from "reax/c", "reax", or "reaxc" to "reaxff" 2021-07-21 21:52:25 -04:00
Axel Kohlmeyer cf3bf374fa
Merge branch 'master' into refactor-reaxff-parser 2021-07-21 00:30:53 -04:00
Axel Kohlmeyer 6604508b55
Merge branch 'master' into collected-small-changes 2021-07-20 19:39:10 -04:00
Axel Kohlmeyer 96389213ab
Merge pull request #2788 from jtclemm/track-contacts 
Track properties of pair interactions
 2021-07-20 19:38:21 -04:00
Axel Kohlmeyer 8a4820a033
add data/units comments to example quip potential files 2021-07-20 19:31:52 -04:00
Axel Kohlmeyer 63794aa698
Merge branch 'master' into track-contacts 
# Conflicts:
#	doc/src/Packages_details.rst
#	src/DIELECTRIC/pair_coul_cut_dielectric.h
#	src/MISC/fix_pair_tracker.cpp
#	src/MISC/fix_pair_tracker.h
#	src/MISC/pair_tracker.cpp
#	src/MISC/pair_tracker.h
#	src/pair_tracker.h
 2021-07-20 16:19:38 -04:00
Oliver Henrich 15b3b6445e Updated tests and documentation, added warning message 2021-07-19 11:22:06 +01:00
Oliver Henrich b7a17dc25d Added warning message in documentation and dsDNA ring test in examples 2021-07-16 12:57:21 +01:00
Axel Kohlmeyer 741e13743c
Merge branch 'master' into refactor-reaxff-parser 2021-07-15 17:23:56 -04:00
Oliver Henrich e99b8ed07c Merge branch 'master' into cg-dna 2021-07-15 13:37:24 +01:00
Oliver Henrich 0f0059269d Modified data_bonds_post() and calling structure 2021-07-15 13:36:40 +01:00
Axel Kohlmeyer 757e2f8cff
Merge branch 'master' into refactor-reaxff-parser 
# Conflicts:
#	doc/src/fix_qeq_reax.rst
#	src/OPENMP/reaxc_bond_orders_omp.h
#	src/OPENMP/reaxc_bonds_omp.h
#	src/OPENMP/reaxc_forces_omp.h
#	src/OPENMP/reaxc_hydrogen_bonds_omp.h
#	src/OPENMP/reaxc_init_md_omp.cpp
#	src/OPENMP/reaxc_init_md_omp.h
#	src/OPENMP/reaxc_multi_body_omp.h
#	src/OPENMP/reaxc_nonbonded_omp.h
#	src/OPENMP/reaxc_torsion_angles_omp.h
#	src/OPENMP/reaxc_valence_angles_omp.h
#	src/OPENMP/reaxff_omp.h
#	src/Purge.list
#	src/QEQ/fix_qeq.cpp
#	src/QEQ/fix_qeq.h
#	src/QEQ/fix_qeq_dynamic.cpp
#	src/QEQ/fix_qeq_fire.cpp
#	src/REAXFF/fix_qeq_reax.cpp
#	src/REAXFF/reaxc_allocate.h
#	src/REAXFF/reaxc_bond_orders.h
#	src/REAXFF/reaxc_bonds.h
#	src/REAXFF/reaxc_control.h
#	src/REAXFF/reaxc_defs.h
#	src/REAXFF/reaxc_ffield.h
#	src/REAXFF/reaxc_forces.h
#	src/REAXFF/reaxc_hydrogen_bonds.h
#	src/REAXFF/reaxc_init_md.cpp
#	src/REAXFF/reaxc_init_md.h
#	src/REAXFF/reaxc_io_tools.cpp
#	src/REAXFF/reaxc_io_tools.h
#	src/REAXFF/reaxc_list.h
#	src/REAXFF/reaxc_lookup.h
#	src/REAXFF/reaxc_multi_body.h
#	src/REAXFF/reaxc_nonbonded.h
#	src/REAXFF/reaxc_reset_tools.h
#	src/REAXFF/reaxc_system_props.cpp
#	src/REAXFF/reaxc_system_props.h
#	src/REAXFF/reaxc_tool_box.h
#	src/REAXFF/reaxc_torsion_angles.h
#	src/REAXFF/reaxc_traj.cpp
#	src/REAXFF/reaxc_traj.h
#	src/REAXFF/reaxc_types.h
#	src/REAXFF/reaxc_valence_angles.h
#	src/REAXFF/reaxc_vector.cpp
#	src/REAXFF/reaxc_vector.h
#	src/REAXFF/reaxff_api.h
#	src/REAXFF/reaxff_defs.h
#	src/REAXFF/reaxff_inline.h
#	src/REAXFF/reaxff_types.h
#	src/text_file_reader.cpp
#	src/text_file_reader.h
#	unittest/force-styles/tests/atomic-pair-reax_c.yaml
#	unittest/force-styles/tests/atomic-pair-reax_c_lgvdw.yaml
#	unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml
 2021-07-12 14:25:47 -04:00
Axel Kohlmeyer 41a434ae1f
fix compilation issues with new/old Intel compilers 2021-07-11 14:09:17 -04:00
Axel Kohlmeyer b2a396da3c
Merge pull request #2828 from tomswinburne/snap-scale 
Adding scale parameter to pair/snap for fix/adapt
 2021-07-07 16:10:11 -04:00
Oliver Henrich 39bd342913 Resolved conflict 2021-07-07 10:04:05 +01:00
tomswinburne 71f82e81d7 Merge branch 'snap-scale' into fm 2021-07-06 17:23:24 +02:00
tomswinburne 3675bef2b0 doc 2021-07-06 14:06:27 +02:00
Oliver Henrich 4b81802ae8 Created new feature branch for PR as per request 2021-07-05 16:07:40 +01:00
Axel Kohlmeyer 430e7e962f
Merge branch 'master' into dielectric-updates 
# Conflicts:
#	src/DIELECTRIC/Install.sh
#	src/DIELECTRIC/pppm_disp_dielectric.cpp
#	src/DIELECTRIC/pppm_disp_dielectric.h
 2021-07-03 15:27:57 -04:00
Trung Nguyen 021e8a404d Updated example data files 2021-07-02 12:20:26 -05:00
Axel Kohlmeyer 58196d57f1
New package DPD-BASIC with pair styles dpd, dpd/tstat, dpd/ext, dpd/ext/tstat 2021-07-01 00:51:55 -04:00
Axel Kohlmeyer 16002ddb54
rename some more example folders 2021-06-29 21:48:57 -04:00
Axel Kohlmeyer 9d208c9ebd
rename some examples folders 2021-06-29 20:25:18 -04:00
Axel Kohlmeyer 878795e64a
bulk rename of remaining USER- packages 2021-06-29 20:12:59 -04:00
Axel Kohlmeyer 1dc25b0e10
rename USER-OMP to OPENMP 2021-06-29 17:48:22 -04:00
Axel Kohlmeyer c085e55695
rename USER-SMD package to MACHDYN 2021-06-29 17:19:39 -04:00
Axel Kohlmeyer 8bf6805e1d
rename USER-LB to LATBOLTZ 2021-06-29 17:07:14 -04:00
Axel Kohlmeyer dc3efd17d2
rename USER-MEAMC to MEAM and pair style meam/c to meam (keeping meam/c as an alias) 2021-06-29 16:59:05 -04:00
Axel Kohlmeyer efaec31a84
rename USER-CGDNA and USER-CGSDK to CG-DNA and CG-SDK 2021-06-29 15:28:27 -04:00
Axel Kohlmeyer 7390d8e344
remove bogus folder 2021-06-29 11:31:31 -04:00
Axel Kohlmeyer 4342987043
rename example folders 2021-06-29 11:23:47 -04:00
Axel Kohlmeyer 8f60a54656
update USER-RANN example to run faster and provide reference logs 2021-06-22 12:27:05 -04:00
Axel Kohlmeyer ddc596170e
Merge pull request #2803 from akohlmey/collected-small-changes 
Collected small changes
 2021-06-21 12:59:16 -04:00
Axel Kohlmeyer a90a48c038
update ASPHERE box/srd example 2021-06-17 10:35:07 -04:00
Axel Kohlmeyer 5a511c2e92
whitespace 2021-06-17 09:56:14 -04:00
macstein ec0f47642a delete old log files 2021-06-14 11:44:05 -07:00
macstein 6a4420ba5c updated log files from the latested run 2021-06-14 11:40:45 -07:00
Axel Kohlmeyer 84d04752d3
update log files. make Si example (much) smaller 2021-06-13 17:40:00 -04:00
macstein e64ec4647a
Delete dump.myforce.3 2021-06-09 20:45:06 -07:00
macstein 06aa6b737e
Delete dump.myforce.2 2021-06-09 20:44:56 -07:00
macstein 399de7dbf8
Delete dump.myforce.1 2021-06-09 20:44:45 -07:00
macstein b4e9e99067
Delete dump.myforce.0 2021-06-09 20:44:32 -07:00
macstein 72ae091aa6 Merge remote-tracking branch 'upstream/master' into mliap_so3_ver2 
To have a fetch
 2021-06-09 20:31:46 -07:00
macstein 75fd4e9eec update 2021-06-09 16:59:59 -07:00
Axel Kohlmeyer 13b8c63e7a
Merge branch 'master' into user-dielectric 2021-06-05 11:14:44 -04:00
Axel Kohlmeyer 5f4bd99544
Merge branch 'master' into track-contacts 2021-06-04 08:42:51 -04:00
jtclemm 80f28e7fa9 fixing merge conflicts, update to master 2021-06-02 12:33:37 -06:00
jtclemm 77f009126a Fixing comments and log files 2021-06-02 12:12:17 -06:00
Trung Nguyen b9e9dda1ab Updated example input scripts, data files and README 2021-06-02 12:03:46 -05:00