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base: tx258:patch_31Jul2019
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tx258:develop tx258:maintenance tx258:granular-triangles tx258:release tx258:stable tx258:rigid-shear tx258:mala tx258:comm-brick-direct tx258:nwchem tx258:coulomb-refactoring tx258:subversion
tx258:patch_12Jun2025 tx258:stable_29Aug2024_update3 tx258:patch_2Apr2025 tx258:stable_29Aug2024_update2 tx258:patch_4Feb2025 tx258:patch_19Nov2024 tx258:stable_29Aug2024_update1 tx258:stable_29Aug2024 tx258:patch_29Aug2024 tx258:stable_2Aug2023_update4 tx258:patch_2Aug2023_update4 tx258:patch_27Jun2024 tx258:patch_17Apr2024 tx258:stable_2Aug2023_update3 tx258:patch_2Aug2023_update3 tx258:patch_7Feb2024_update1 tx258:patch_7Feb2024 tx258:stable_2Aug2023_update2 tx258:patch_2Aug2023_update2 tx258:patch_21Nov2023 tx258:lammps-gui-v1.5 tx258:lammps-gui-v1.2 tx258:patch_2Aug2023_update1 tx258:stable_2Aug2023_update1 tx258:stable_2Aug2023 tx258:patch_2Aug2023 tx258:patch_15Jun2023 tx258:patch_23Jun2022_update4 tx258:stable_23Jun2022_update4 tx258:patch_28Mar2023_update1 tx258:patch_28Mar2023 tx258:patch_23Jun2022_update3 tx258:stable_23Jun2022_update3 tx258:patch_8Feb2023 tx258:patch_22Dec2022 tx258:patch_23Jun2022_update2 tx258:stable_23Jun2022_update2 tx258:patch_3Nov2022 tx258:patch_15Sep2022 tx258:stable_23Jun2022_update1 tx258:patch_23Jun2022_update1 tx258:patch_3Aug2022 tx258:stable_23Jun2022 tx258:patch_23Jun2022 tx258:patch_2Jun2022 tx258:patch_4May2022 tx258:patch_29Sep2021_update3 tx258:patch_24Mar2022 tx258:stable_29Sep2021_update3 tx258:patch_17Feb2022 tx258:patch_7Jan2022 tx258:patch_29Sep2021_update2 tx258:stable_29Sep2021_update2 tx258:patch_14Dec2021 tx258:patch_29Sep2021_update1 tx258:stable_29Sep2021_update1 tx258:patch_27Oct2021 tx258:stable_29Sep2021 tx258:patch_29Sep2021 tx258:patch_20Sep2021 tx258:patch_31Aug2021 tx258:patch_30Jul2021 tx258:patch_28Jul2021 tx258:patch_2Jul2021 tx258:patch_27May2021 tx258:patch_14May2021 tx258:patch_8Apr2021 tx258:patch_10Mar2021 tx258:patch_10Feb2021 tx258:patch_24Dec2020 tx258:patch_30Nov2020 tx258:stable_29Oct2020 tx258:patch_29Oct2020 tx258:patch_22Oct2020 tx258:patch_9Oct2020 tx258:patch_18Sep2020 tx258:patch_24Aug2020 tx258:patch_21Aug2020 tx258:patch_21Jul2020 tx258:patch_30Jun2020 tx258:patch_15Jun2020 tx258:patch_2Jun2020 tx258:patch_5May2020 tx258:patch_15Apr2020 tx258:patch_19Mar2020 tx258:stable_3Mar2020 tx258:patch_3Mar2020 tx258:patch_27Feb2020 tx258:patch_18Feb2020 tx258:patch_4Feb2020 tx258:patch_24Jan2020 tx258:patch_9Jan2020 tx258:patch_20Nov2019 tx258:patch_30Oct2019 tx258:patch_19Sep2019 tx258:stable_7Aug2019 tx258:patch_7Aug2019 tx258:patch_6Aug2019 tx258:patch_2Aug2019 tx258:patch_31Jul2019 tx258:patch_19Jul2019 tx258:patch_18Jun2019 tx258:stable_5Jun2019 tx258:patch_5Jun2019 tx258:patch_31May2019 tx258:patch_15May2019 tx258:patch_30Apr2019 tx258:patch_29Mar2019 tx258:patch_28Feb2019 tx258:patch_8Feb2019 tx258:patch_1Feb2019 tx258:patch_4Jan2019 tx258:patch_12Dec2018 tx258:stable_12Dec2018 tx258:patch_7Dec2018 tx258:patch_27Nov2018 tx258:patch_15Nov2018 tx258:patch_9Nov2018 tx258:patch_24Oct2018 tx258:patch_10Oct2018 tx258:patch_18Sep2018 tx258:patch_5Sep2018 tx258:patch_31Aug2018 tx258:stable_22Aug2018 tx258:patch_22Aug2018 tx258:patch_16Aug2018 tx258:patch_2Aug2018 tx258:patch_16Jul2018 tx258:patch_29Jun2018 tx258:patch_22Jun2018 tx258:patch_11May2018 tx258:patch_20Apr2018 tx258:patch_30Mar2018 tx258:patch_16Mar2018 tx258:stable_16Mar2018 tx258:patch_8Mar2018 tx258:patch_22Feb2018 tx258:patch_5Feb2018 tx258:patch_17Jan2018 tx258:patch_23Oct2017 tx258:patch_22Sep2017 tx258:patch_1Sep2017 tx258:patch_17Aug2017 tx258:stable_11Aug2017 tx258:patch_11Aug2017 tx258:patch_10Aug2017 tx258:patch_24Jul2017 tx258:patch_6Jul2017 tx258:patch_23Jun2017 tx258:patch_20Jun2017 tx258:patch_19May2017 tx258:patch_4May2017 tx258:patch_13Apr2017 tx258:patch_11Apr2017 tx258:patch_31Mar2017 tx258:stable_31Mar2017 tx258:patch_28Mar2017 tx258:patch_24Mar2017 tx258:patch_17Mar2017 tx258:patch_10Mar2017 tx258:patch_7Mar2017 tx258:patch_21Feb2017 tx258:patch_13Feb2017 tx258:patch_26Jan2017 tx258:patch_20Jan2017 tx258:patch_17Jan2017 tx258:patch_9Jan2017 tx258:patch_6Jan2017 tx258:patch_21Dec2016 tx258:patch_17Dec2016 tx258:patch_16Dec2016 tx258:patch_13Dec2016 tx258:patch_30Nov2016 tx258:patch_22Nov2016 tx258:stable_17Nov2016 tx258:patch_17Nov2016 tx258:patch_9Nov2016 tx258:stable_5Nov2016 tx258:patch_5Nov2016 tx258:stable_4Nov2016 tx258:patch_4Nov2016 tx258:patch_27Oct2016 tx258:patch_20Oct2016 tx258:patch_19Oct2016 tx258:patch_18Oct2016 tx258:patch_13Oct2016 tx258:patch_12Oct2016 tx258:patch_11Oct2016 tx258:patch_6Oct2016 tx258:patch_5Oct2016 tx258:patch_30Sep2016 tx258:patch_29Sep2016 tx258:patch_28Sep2016 tx258:patch_26Sep2016 tx258:patch_21Sep2016 tx258:patch_20Sep2016 tx258:patch_15Sep2016 tx258:r15407 tx258:r15061 tx258:r14624 tx258:r14304 tx258:r13864 tx258:r13475 tx258:r13095 tx258:r12824 tx258:r12671 tx258:r12430 tx258:r12164 tx258:r11423
..
compare: tx258:patch_2Aug2019
Branches Tags
tx258:develop tx258:maintenance tx258:granular-triangles tx258:release tx258:stable tx258:rigid-shear tx258:mala tx258:comm-brick-direct tx258:nwchem tx258:coulomb-refactoring tx258:subversion
tx258:patch_12Jun2025 tx258:stable_29Aug2024_update3 tx258:patch_2Apr2025 tx258:stable_29Aug2024_update2 tx258:patch_4Feb2025 tx258:patch_19Nov2024 tx258:stable_29Aug2024_update1 tx258:stable_29Aug2024 tx258:patch_29Aug2024 tx258:stable_2Aug2023_update4 tx258:patch_2Aug2023_update4 tx258:patch_27Jun2024 tx258:patch_17Apr2024 tx258:stable_2Aug2023_update3 tx258:patch_2Aug2023_update3 tx258:patch_7Feb2024_update1 tx258:patch_7Feb2024 tx258:stable_2Aug2023_update2 tx258:patch_2Aug2023_update2 tx258:patch_21Nov2023 tx258:lammps-gui-v1.5 tx258:lammps-gui-v1.2 tx258:patch_2Aug2023_update1 tx258:stable_2Aug2023_update1 tx258:stable_2Aug2023 tx258:patch_2Aug2023 tx258:patch_15Jun2023 tx258:patch_23Jun2022_update4 tx258:stable_23Jun2022_update4 tx258:patch_28Mar2023_update1 tx258:patch_28Mar2023 tx258:patch_23Jun2022_update3 tx258:stable_23Jun2022_update3 tx258:patch_8Feb2023 tx258:patch_22Dec2022 tx258:patch_23Jun2022_update2 tx258:stable_23Jun2022_update2 tx258:patch_3Nov2022 tx258:patch_15Sep2022 tx258:stable_23Jun2022_update1 tx258:patch_23Jun2022_update1 tx258:patch_3Aug2022 tx258:stable_23Jun2022 tx258:patch_23Jun2022 tx258:patch_2Jun2022 tx258:patch_4May2022 tx258:patch_29Sep2021_update3 tx258:patch_24Mar2022 tx258:stable_29Sep2021_update3 tx258:patch_17Feb2022 tx258:patch_7Jan2022 tx258:patch_29Sep2021_update2 tx258:stable_29Sep2021_update2 tx258:patch_14Dec2021 tx258:patch_29Sep2021_update1 tx258:stable_29Sep2021_update1 tx258:patch_27Oct2021 tx258:stable_29Sep2021 tx258:patch_29Sep2021 tx258:patch_20Sep2021 tx258:patch_31Aug2021 tx258:patch_30Jul2021 tx258:patch_28Jul2021 tx258:patch_2Jul2021 tx258:patch_27May2021 tx258:patch_14May2021 tx258:patch_8Apr2021 tx258:patch_10Mar2021 tx258:patch_10Feb2021 tx258:patch_24Dec2020 tx258:patch_30Nov2020 tx258:stable_29Oct2020 tx258:patch_29Oct2020 tx258:patch_22Oct2020 tx258:patch_9Oct2020 tx258:patch_18Sep2020 tx258:patch_24Aug2020 tx258:patch_21Aug2020 tx258:patch_21Jul2020 tx258:patch_30Jun2020 tx258:patch_15Jun2020 tx258:patch_2Jun2020 tx258:patch_5May2020 tx258:patch_15Apr2020 tx258:patch_19Mar2020 tx258:stable_3Mar2020 tx258:patch_3Mar2020 tx258:patch_27Feb2020 tx258:patch_18Feb2020 tx258:patch_4Feb2020 tx258:patch_24Jan2020 tx258:patch_9Jan2020 tx258:patch_20Nov2019 tx258:patch_30Oct2019 tx258:patch_19Sep2019 tx258:stable_7Aug2019 tx258:patch_7Aug2019 tx258:patch_6Aug2019 tx258:patch_2Aug2019 tx258:patch_31Jul2019 tx258:patch_19Jul2019 tx258:patch_18Jun2019 tx258:stable_5Jun2019 tx258:patch_5Jun2019 tx258:patch_31May2019 tx258:patch_15May2019 tx258:patch_30Apr2019 tx258:patch_29Mar2019 tx258:patch_28Feb2019 tx258:patch_8Feb2019 tx258:patch_1Feb2019 tx258:patch_4Jan2019 tx258:patch_12Dec2018 tx258:stable_12Dec2018 tx258:patch_7Dec2018 tx258:patch_27Nov2018 tx258:patch_15Nov2018 tx258:patch_9Nov2018 tx258:patch_24Oct2018 tx258:patch_10Oct2018 tx258:patch_18Sep2018 tx258:patch_5Sep2018 tx258:patch_31Aug2018 tx258:stable_22Aug2018 tx258:patch_22Aug2018 tx258:patch_16Aug2018 tx258:patch_2Aug2018 tx258:patch_16Jul2018 tx258:patch_29Jun2018 tx258:patch_22Jun2018 tx258:patch_11May2018 tx258:patch_20Apr2018 tx258:patch_30Mar2018 tx258:patch_16Mar2018 tx258:stable_16Mar2018 tx258:patch_8Mar2018 tx258:patch_22Feb2018 tx258:patch_5Feb2018 tx258:patch_17Jan2018 tx258:patch_23Oct2017 tx258:patch_22Sep2017 tx258:patch_1Sep2017 tx258:patch_17Aug2017 tx258:stable_11Aug2017 tx258:patch_11Aug2017 tx258:patch_10Aug2017 tx258:patch_24Jul2017 tx258:patch_6Jul2017 tx258:patch_23Jun2017 tx258:patch_20Jun2017 tx258:patch_19May2017 tx258:patch_4May2017 tx258:patch_13Apr2017 tx258:patch_11Apr2017 tx258:patch_31Mar2017 tx258:stable_31Mar2017 tx258:patch_28Mar2017 tx258:patch_24Mar2017 tx258:patch_17Mar2017 tx258:patch_10Mar2017 tx258:patch_7Mar2017 tx258:patch_21Feb2017 tx258:patch_13Feb2017 tx258:patch_26Jan2017 tx258:patch_20Jan2017 tx258:patch_17Jan2017 tx258:patch_9Jan2017 tx258:patch_6Jan2017 tx258:patch_21Dec2016 tx258:patch_17Dec2016 tx258:patch_16Dec2016 tx258:patch_13Dec2016 tx258:patch_30Nov2016 tx258:patch_22Nov2016 tx258:stable_17Nov2016 tx258:patch_17Nov2016 tx258:patch_9Nov2016 tx258:stable_5Nov2016 tx258:patch_5Nov2016 tx258:stable_4Nov2016 tx258:patch_4Nov2016 tx258:patch_27Oct2016 tx258:patch_20Oct2016 tx258:patch_19Oct2016 tx258:patch_18Oct2016 tx258:patch_13Oct2016 tx258:patch_12Oct2016 tx258:patch_11Oct2016 tx258:patch_6Oct2016 tx258:patch_5Oct2016 tx258:patch_30Sep2016 tx258:patch_29Sep2016 tx258:patch_28Sep2016 tx258:patch_26Sep2016 tx258:patch_21Sep2016 tx258:patch_20Sep2016 tx258:patch_15Sep2016 tx258:r15407 tx258:r15061 tx258:r14624 tx258:r14304 tx258:r13864 tx258:r13475 tx258:r13095 tx258:r12824 tx258:r12671 tx258:r12430 tx258:r12164 tx258:r11423

47 Commits
patch_31Ju ... patch_2Aug

Author SHA1 Message Date
Axel Kohlmeyer
aff5f06e8f Merge pull request #1612 from akohlmey/new_version 
Step version string for next patch release
 2019-08-02 14:27:13 -04:00
Axel Kohlmeyer
bd3ffe1321 Merge pull request #1603 from eagunn/iss1572clean 
Iss1572clean: Clean fix for error handling, clarify data requirements for fix bocs input
 2019-08-02 10:43:30 -04:00
Axel Kohlmeyer
11198e9d29 Merge pull request #1607 from giacomofiorin/colvars-update 
Update Colvars to version 2019-08-01
 2019-08-02 10:43:13 -04:00
Axel Kohlmeyer
a857e7f790 Merge pull request #1608 from wmbrownIntel/intel-eam-eatom-fix 
Bug fix for eam/intel per-atom energy calculation.
 2019-08-02 10:42:54 -04:00
Axel Kohlmeyer
9c691ddd0f Merge pull request #1610 from wmbrownIntel/intel-ncache-alias-fix 
Bug fixes for use of uninitialized variable and strict-aliasing in USER-INTEL
 2019-08-02 10:42:37 -04:00
Axel Kohlmeyer
828ddfd957 Merge pull request #1611 from evoyiatzis/patch-1 
small clean-up of fix.txt
 2019-08-02 10:42:20 -04:00
Axel Kohlmeyer
7ba6b8a06a Merge pull request #1604 from akohlmey/timeout-for-replica 
Add support for timeouts to temper commands and a few small fixes
 2019-08-02 10:41:44 -04:00
Anne Gunn
d750cc02c0 Changed the code in the read_F_table function to conform to the "expected behavior" description in #1572. Adopted a best-of-both-worlds approach, though, and processed the whole input file all the way through, emitting a message for each problem found, before issuing a final error message to stop processing. Updated doc to clarify requirement for uniform spacing of pressure correction points. 2019-08-02 08:46:04 -04:00
Axel Kohlmeyer
9ed43e55f0 add some more descriptions for fixes to list of style in fix command docs 2019-08-02 08:41:34 -04:00
Axel Kohlmeyer
8fd28cd78d fix typo 2019-08-02 08:40:59 -04:00
Axel Kohlmeyer
b5f19b93c2 Step version string for next patch release 2019-08-02 05:15:29 -04:00
Evangelos Voyiatzis
5076f1a36c small clean-up of fix.txt 2019-08-02 10:55:18 +02:00
Axel Kohlmeyer
f61cd68ca4 add missing parenthesis 2019-08-01 20:43:33 -04:00
Axel Kohlmeyer
5b4b418289 use check_language() instead of enable_language() to get fortran compiler name 2019-08-01 18:24:14 -04:00
Axel Kohlmeyer
8df7f51470 Merge branch 'master' into timeout-for-replica 2019-08-01 16:56:49 -04:00
Axel Kohlmeyer
f9e34825f0 workaround for xcode oddity with compiling voro++ 2019-08-01 16:42:52 -04:00
Giacomo Fiorin
52e2db44a1 Update Colvars to version 2019-08-01 
One new feature (geometric path variables) and bugfixes.

Minimize occurrence of file-read errors in multiple-walker metadynamics
https://github.com/Colvars/colvars/pull/276

Better error messages for RMSD
https://github.com/Colvars/colvars/pull/272

Ensemble-biased metadynamics documentation
https://github.com/Colvars/colvars/pull/261

Fix bug on multiple walkers metadynamics, pmf included twice
https://github.com/Colvars/colvars/pull/259

Implementation of the geometric path collective variables (C++11-only feature)
https://github.com/Colvars/colvars/pull/249
 2019-08-01 15:15:58 -04:00
Axel Kohlmeyer
de366c27e2 Merge pull request #1606 from oywg11/fix-ILP-bug 
Fix a communication bug of potential #839
 2019-08-01 15:01:13 -04:00
Axel Kohlmeyer
5fd323fe32 simplify example folder for ilp/graphene/hbn potential 
- flatten directory structure
- remove CPU time and reduce excess precision from output
- delete redundant and unused files
- regenerate reference outputs
 2019-08-01 14:24:47 -04:00
Axel Kohlmeyer
64b682b9f9 library compilation fix for clang with exceptions and -DLAMMPS_BIGBIG 2019-08-01 13:40:50 -04:00
Axel Kohlmeyer
083841ab2a another compilation fix 2019-08-01 13:34:05 -04:00
Axel Kohlmeyer
fa6a990536 reduce output precision to default and don't output per-step cpu time 2019-08-01 13:31:52 -04:00
Axel Kohlmeyer
73d2b824bd fix compilation issue of library.cpp with exceptions enabled 2019-08-01 13:31:13 -04:00
Axel Kohlmeyer
e17e6bb45d Merge pull request #1605 from akohlmey/fix-compilation-errors 
Fix some compilation errors
 2019-08-01 11:24:30 -04:00
Axel Kohlmeyer
2fe4a6490c restore include file cleanup changes 2019-08-01 11:20:06 -04:00
Axel Kohlmeyer
5fe457667e restore showing references to potential files without pathnames 2019-08-01 11:19:39 -04:00
oywg11
02511a0ae5 Merge branch 'fix-compilation-errors' of https://github.com/akohlmey/lammps into fix-ILP-bug 2019-08-01 17:40:01 +03:00
oywg11
76bac4cedc Fix communication bug of ILP 2019-08-01 16:39:42 +03:00
oywg11
8f5cd8661f Fix communication bug of ILP 2019-08-01 16:38:19 +03:00
Michael Brown
e57c3c04d0 Bug fixes for use of uninitialized variable and strict-aliasing in USER-INTEL. 2019-08-01 05:32:18 -07:00
Axel Kohlmeyer
c967c09561 correct compilation error with exceptions enabled in main.cpp 2019-08-01 08:14:27 -04:00
Axel Kohlmeyer
a6bd86eb77 make USER-OMP code compatible with pre-c++ 11 compilers again 2019-08-01 08:14:03 -04:00
Axel Kohlmeyer
e3c91626c8 need to include update.h when exceptions are enabled 2019-08-01 07:07:21 -04:00
Axel Kohlmeyer
2a74832a1e protect MPI library version detection from incompatible MPI libraries 2019-08-01 07:04:24 -04:00
Axel Kohlmeyer
86e3740fb3 use more common syntax for CPP's "defined" keyword 2019-08-01 07:03:51 -04:00
Axel Kohlmeyer
892e4759df protect Spectrum MPI detection from failing to compile with MPI libraries implementing MPI version 2 or 1 2019-08-01 07:02:55 -04:00
Axel Kohlmeyer
207976f4e9 avoid abort when timeout appears in temper commands 2019-08-01 06:11:05 -04:00
Michael Brown
074ae06b36 Bug fix for eam/intel per-atom energy calculation. 2019-08-01 02:19:49 -07:00
Axel Kohlmeyer
75c1e28566 fix typo 2019-07-31 23:28:57 -04:00
Axel Kohlmeyer
58404946db add timer timeout support to temper commands 2019-07-31 23:26:13 -04:00
Axel Kohlmeyer
d09ca91627 Merge pull request #1599 from rbberger/collected-small-changes 
Collected small changes
 2019-07-31 19:13:41 -04:00
Axel Kohlmeyer
e89cedbd99 Merge pull request #1601 from akohlmey/cmake-list-portability 
Improve compatibility to older CMake versions when building/installing LAMMPS library and headers
 2019-07-31 12:19:41 -04:00
Axel Kohlmeyer
4011f6650d first step of adding timeout support to temper commands 2019-07-31 05:05:17 -04:00
Axel Kohlmeyer
0fa9cd5004 use utils::strmatch to simplify checks for compatible thermostat/barostat fixes 2019-07-31 05:03:59 -04:00
Richard Berger
3cc8508795 Add missing definition of NULL in USER-PTM header 2019-07-31 03:22:22 -04:00
Richard Berger
da3b91a744 Remove not existing files from USER-PHONON Install.sh 2019-07-31 03:11:44 -04:00
Axel Kohlmeyer
bc79412203 list(TRANSFORM ...) is not portable to older versions of cmake. work around it. 2019-07-30 22:54:02 -04:00
89 changed files with 9142 additions and 5636 deletions
Expand all files Collapse all files

61
cmake/CMakeLists.txt
View File

@ -497,37 +497,36 @@ if(BUILD_LIB)
add_dependencies(lammps ${LAMMPS_DEPS})
endif()
set(LAMMPS_CXX_HEADERS
angle.h
atom.h
bond.h
citeme.h
comm.h
compute.h
dihedral.h
domain.h
error.h
fix.h
force.h
group.h
improper.h
input.h
kspace.h
lammps.h
lattice.h
lmppython.h
memory.h
modify.h
neighbor.h
neigh_list.h
output.h
pair.h
pointers.h
region.h
timer.h
universe.h
update.h
variable.h)
list(TRANSFORM LAMMPS_CXX_HEADERS PREPEND ${LAMMPS_SOURCE_DIR}/)
${LAMMPS_SOURCE_DIR}/angle.h
${LAMMPS_SOURCE_DIR}/atom.h
${LAMMPS_SOURCE_DIR}/bond.h
${LAMMPS_SOURCE_DIR}/citeme.h
${LAMMPS_SOURCE_DIR}/comm.h
${LAMMPS_SOURCE_DIR}/compute.h
${LAMMPS_SOURCE_DIR}/dihedral.h
${LAMMPS_SOURCE_DIR}/domain.h
${LAMMPS_SOURCE_DIR}/error.h
${LAMMPS_SOURCE_DIR}/fix.h
${LAMMPS_SOURCE_DIR}/force.h
${LAMMPS_SOURCE_DIR}/group.h
${LAMMPS_SOURCE_DIR}/improper.h
${LAMMPS_SOURCE_DIR}/input.h
${LAMMPS_SOURCE_DIR}/kspace.h
${LAMMPS_SOURCE_DIR}/lammps.h
${LAMMPS_SOURCE_DIR}/lattice.h
${LAMMPS_SOURCE_DIR}/lmppython.h
${LAMMPS_SOURCE_DIR}/memory.h
${LAMMPS_SOURCE_DIR}/modify.h
${LAMMPS_SOURCE_DIR}/neighbor.h
${LAMMPS_SOURCE_DIR}/neigh_list.h
${LAMMPS_SOURCE_DIR}/output.h
${LAMMPS_SOURCE_DIR}/pair.h
${LAMMPS_SOURCE_DIR}/pointers.h
${LAMMPS_SOURCE_DIR}/region.h
${LAMMPS_SOURCE_DIR}/timer.h
${LAMMPS_SOURCE_DIR}/universe.h
${LAMMPS_SOURCE_DIR}/update.h
${LAMMPS_SOURCE_DIR}/variable.h)
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})

8
cmake/Modules/Packages/KIM.cmake
View File

@ -20,9 +20,13 @@ if(PKG_KIM)
message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
endif()
message(STATUS "KIM-API download requested - we will build our own")
enable_language(C)
enable_language(Fortran)
include(CheckLanguage)
include(ExternalProject)
enable_language(C)
check_language(Fortran)
if(NOT CMAKE_Fortran_COMPILER)
message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
endif()
ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz
URL_MD5 6ac52e14ef52967fc7858220b208cba5

8
cmake/Modules/Packages/VORONOI.cmake
View File

@ -18,8 +18,12 @@ if(PKG_VORONOI)
else()
set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
endif()
string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
if(APPLE)
get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
else()
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
endif()
ExternalProject_Add(voro_build
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz

2
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "31 July 2019" "2019-07-31"
.TH LAMMPS "2 August 2019" "2019-08-02"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

BIN
doc/src/Eqs/pair_kolmogorov_crespi_full.jpg
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2
doc/src/Eqs/pair_kolmogorov_crespi_full.tex
View File

@ -27,7 +27,7 @@
V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
\rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
\rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{j})^2 \\[15pt]
f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n}
\end{eqnarray*}
\endgroup
\end{document}

4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="31 Jul 2019 version">
<META NAME="docnumber" CONTENT="2 Aug 2019 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
:line
LAMMPS Documentation :c,h1
31 Jul 2019 version :c,h2
2 Aug 2019 version :c,h2
"What is a LAMMPS version?"_Manual_version.html

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doc/src/fix.txt
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@ -165,40 +165,40 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
"adapt"_fix_adapt.html - change a simulation parameter over time
"adapt/fep"_fix_adapt_fep.html -
"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt
"addforce"_fix_addforce.html - add a force to each atom
"addtorque"_fix_addtorque.html -
"addtorque"_fix_addtorque.html - add a torque to a group of atoms
"append/atoms"_fix_append_atoms.html - append atoms to a running simulation
"atc"_fix_atc.html -
"atc"_fix_atc.html - initiates a coupled MD/FE simulation
"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
"ave/correlate"_fix_ave_correlate.html - compute/output time correlations
"ave/correlate/long"_fix_ave_correlate_long.html -
"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
"ave/histo/weight"_fix_ave_histo.html -
"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo
"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
"aveforce"_fix_aveforce.html - add an averaged force to each atom
"balance"_fix_balance.html - perform dynamic load-balancing
"bocs"_fix_bocs.html -
"bocs"_fix_bocs.html - NPT style time integration with pressure correction
"bond/break"_fix_bond_break.html - break bonds on the fly
"bond/create"_fix_bond_create.html - create bonds on the fly
"bond/react"_fix_bond_react.html -
"bond/react"_fix_bond_react.html - apply topology changes to model reactions
"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
"box/relax"_fix_box_relax.html - relax box size during energy minimization
"client/md"_fix_client_md.html -
"cmap"_fix_cmap.html -
"colvars"_fix_colvars.html -
"controller"_fix_controller.html -
"client/md"_fix_client_md.html - MD client for client/server simulations
"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
"colvars"_fix_colvars.html - interface to the collective variables “Colvars” library
"controller"_fix_controller.html - apply control loop feedback mechanism
"deform"_fix_deform.html - change the simulation box size/shape
"deposit"_fix_deposit.html - add new atoms above a surface
"dpd/energy"_fix_dpd_energy.html -
"dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics
"drag"_fix_drag.html - drag atoms towards a defined coordinate
"drude"_fix_drude.html -
"drude/transform/direct"_fix_drude_transform.html -
"drude/transform/inverse"_fix_drude_transform.html -
"drude"_fix_drude.html - part of Drude oscillator polarization model
"drude/transform/direct"_fix_drude_transform.html - part of Drude oscillator polarization model
"drude/transform/inverse"_fix_drude_transform.html - part of Drude oscillator polarization model
"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
"edpd/source"_fix_dpd_source.html -
"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations
"efield"_fix_efield.html - impose electric field on system
"ehex"_fix_ehex.html - enhanced heat exchange algorithm
"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
@ -208,27 +208,26 @@ accelerated styles exist.
"eos/table/rx"_fix_eos_table_rx.html -
"evaporate"_fix_evaporate.html - remove atoms from simulation periodically
"external"_fix_external.html - callback to an external driver program
"ffl"_fix_ffl.html -
"filter/corotate"_fix_filter_corotate.html -
"flow/gauss"_fix_flow_gauss.html -
"ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat
"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA
"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux
"freeze"_fix_freeze.html - freeze atoms in a granular simulation
"gcmc"_fix_gcmc.html - grand canonical insertions/deletions
"gld"_fix_gcmc.html - generalized Langevin dynamics integrator
"gld"_fix_gld.html -
"gle"_fix_gle.html -
"gld"_fix_gld.html - generalized Langevin dynamics integrator
"gle"_fix_gle.html - generalized Langevin equation thermostat
"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
"grem"_fix_grem.html -
"grem"_fix_grem.html - implements the generalized replica exchange method
"halt"_fix_halt.html - terminate a dynamics run or minimization
"heat"_fix_heat.html - add/subtract momentum-conserving heat
"hyper/global"_fix_hyper_global.html - global hyperdynamics
"hyper/local"_fix_hyper_local.html - local hyperdynamics
"imd"_fix_imd.html -
"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol
"indent"_fix_indent.html - impose force due to an indenter
"ipi"_fix_ipi.html -
"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
"langevin"_fix_langevin.html - Langevin temperature control
"langevin/drude"_fix_langevin_drude.html -
"langevin/eff"_fix_langevin_eff.html -
"langevin/spin"_fix_langevin_spin.html -
"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators
"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model
"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system
"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
"lb/fluid"_fix_lb_fluid.html -
"lb/momentum"_fix_lb_momentum.html -
@ -236,64 +235,60 @@ accelerated styles exist.
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
"lb/viscous"_fix_lb_viscous.html -
"lineforce"_fix_lineforce.html - constrain atoms to move in a line
"manifoldforce"_fix_manifoldforce.html -
"meso"_fix_meso.html -
"meso"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
"meso/move"_fix_meso_move.html -
"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization
"meso"_fix_meso.html - time integration for SPH/DPDE particles
"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
"meso/stationary"_fix_meso_stationary.html -
"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
"move"_fix_move.html - move atoms in a prescribed fashion
"mscg"_fix_mscg.html -
"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
"msst"_fix_msst.html - multi-scale shock technique (MSST) integration
"mvv/dpd"_fix_mvv_dpd.html -
"mvv/edpd"_fix_mvv_dpd.html -
"mvv/tdpd"_fix_mvv_dpd.html -
"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm
"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
"neb"_fix_neb.html - nudged elastic band (NEB) spring forces
"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
"nph/body"_fix_nph_body.html -
"nph/body"_fix_nve_body.html - NPH for body particles
"nph/eff"_fix_nh_eff.html -
"nph/body"_fix_nph_body.html - NPH for body particles
"nph/eff"_fix_nh_eff.html - NPH for nuclei and electrons in the electron force field model
"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
"npt/body"_fix_npt_body.html -
"npt/body"_fix_nve_body.html - NPT for body particles
"npt/eff"_fix_nh_eff.html -
"npt/body"_fix_npt_body.html - NPT for body particles
"npt/eff"_fix_nh_eff.html - NPT for nuclei and electrons in the electron force field model
"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
"npt/uef"_fix_nh_uef.html -
"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow
"nve"_fix_nve.html - constant NVE time integration
"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces"
"nve/awpmd"_fix_nve_awpmd.html -
"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces
"nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model
"nve/body"_fix_nve_body.html - NVE for body particles
"nve/dot"_fix_nve_dot.html -
"nve/dotc/langevin"_fix_nve_dotc_langevin.html -
"nve/eff"_fix_nve_eff.html -
"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models
"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models
"nve/eff"_fix_nve_eff.html - NVE for nuclei and electrons in the electron force field model
"nve/limit"_fix_nve_limit.html - NVE with limited step length
"nve/line"_fix_nve_line.html - NVE for line segments
"nve/manifold/rattle"_fix_nve_manifold_rattle.html -
"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
"nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
"nve/spin"_fix_nve_spin.html -
"nve/spin"_fix_nve_spin.html - NVE for a spin or spin-lattice system
"nve/tri"_fix_nve_tri.html - NVE for triangles
"nvk"_fix_nvk.html -
"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
"nvk"_fix_nvk.html - constant kinetic energy time integration
"nvt"_fix_nh.html - NVT time integration via Nose/Hoover
"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
"nvt/body"_fix_nve_body.html - NVT for body particles
"nvt/body"_fix_nvt_body.html -
"nvt/eff"_fix_nh_eff.html -
"nvt/body"_fix_nvt_body.html - NVT for body particles
"nvt/eff"_fix_nh_eff.html - NVE for nuclei and electrons in the electron force field model
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
"nvt/sllod/eff"_fix_nvt_sllod_eff.html -
"nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model
"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
"nvt/uef"_fix_nh_uef.html -
"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow
"oneway"_fix_oneway.html - constrain particles on move in one direction
"orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
"orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
"phonon"_fix_phonon.html -
"pimd"_fix_pimd.html -
"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations
"pimd"_fix_pimd.html - Feynman path integral molecular dynamics
"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
"plumed"_fix_plumed.html - wrapper on PLUMED free energy library
"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
@ -302,24 +297,24 @@ accelerated styles exist.
"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
"print"_fix_print.html - print text and variables during a simulation
"property/atom"_fix_property_atom.html - add customized per-atom values
"python/invoke"_fix_python_invoke.html -
"python/move"_fix_python_move.html -
"qbmsst"_fix_qbmsst.html -
"python/invoke"_fix_python_invoke.html - call a Python function during a simulation
"python/move"_fix_python_move.html - call a Python function during a simulation run
"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator
"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
"qeq/point"_fix_qeq.html - charge equilibration via point method
"qeq/reax"_fix_qeq_reax.html -
"qeq/reax"_fix_qeq_reax.html - charge equilibration for ReaxFF potential
"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
"qeq/slater"_fix_qeq.html - charge equilibration via Slater method
"qmmm"_fix_qmmm.html -
"qtb"_fix_qtb.html -
"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling
"qtb"_fix_qtb.html - implement quantum thermal bath scheme
"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
"rhok"_fix_rhok.html -
"rhok"_fix_rhok.html - add bias potential for long-range ordered systems
"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
@ -332,11 +327,11 @@ accelerated styles exist.
"rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
"rx"_fix_rx.html -
"saed/vtk"_fix_saed_vtk.html -
"saed/vtk"_fix_saed_vtk.html -
"setforce"_fix_setforce.html - set the force on each atom
"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
"shardlow"_fix_shardlow.html -
"smd"_fix_smd.html -
"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
"smd"_fix_smd.html - applied a steered MD force to a group
"smd/adjust_dt"_fix_smd_adjust_dt.html -
"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
@ -355,13 +350,13 @@ accelerated styles exist.
"temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
"temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
"temp/rescale/eff"_fix_temp_rescale_eff.html -
"temp/rescale/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model
"tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
"ti/spring"_fix_ti_spring.html -
"tmd"_fix_tmd.html - guide a group of atoms to a new configuration
"ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
"ttm/mod"_fix_ttm.html -
"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options
"tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
"vector"_fix_vector.html - accumulate a global vector every N timesteps
"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
@ -369,7 +364,7 @@ accelerated styles exist.
"wall/body/polygon"_fix_wall_body_polygon.html -
"wall/body/polyhedron"_fix_wall_body_polyhedron.html -
"wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
"wall/ees"_fix_wall_ees.html -
"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles
"wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
"wall/gran/region"_fix_wall_gran_region.html -
"wall/harmonic"_fix_wall.html - harmonic spring wall
@ -379,7 +374,7 @@ accelerated styles exist.
"wall/piston"_fix_wall_piston.html - moving reflective piston wall
"wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
"wall/region"_fix_wall_region.html - use region surface as wall
"wall/region/ees"_fix_wall_ees.html -
"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles
"wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
[Restrictions:]

4
doc/src/fix_bocs.txt
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@ -47,13 +47,13 @@ or {cubic_spline}.
With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
as a function of volume. The file should be formatted so each line has:
as a function of volume. The file must be formatted so each line has:
Volume_i, PressureCorrection_i :pre
Note both the COMMA and the SPACE separating the volume's
value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
must be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using {units real},
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atmospheres. Furthermore, the table should start/end at a

4
doc/src/fix_rhok.txt
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@ -39,8 +39,8 @@ An example of using the interface pinning method is located in the
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
was built with that package. See the "Build
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]

2
doc/src/pair_coul_shield.txt
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@ -13,7 +13,7 @@ pair_style coul/shield command :h3
pair_style coul/shield cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function
tap_flag = 0/1 to turn off/on the taper function :ul
[Examples:]

28
doc/src/pair_ilp_graphene_hbn.txt
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@ -13,17 +13,17 @@ pair_style ilp/graphene/hbn command :h3
pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function
tap_flag = 0/1 to turn off/on the taper function :ul
[Examples:]
pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre
pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
pair_coeff * * rebo CH.rebo NULL NULL C
pair_coeff * * tersoff BNC.tersoff B N NULL
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
pair_coeff * * rebo CH.rebo NULL NULL C
pair_coeff * * tersoff BNC.tersoff B N NULL
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.695
pair_coeff 2 2 coul/shield 0.69 :pre
@ -85,6 +85,22 @@ be found in "(Ouyang)"_#Ouyang.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the "compute
pair"_compute_pair.html command as a vector of values of length 2.
The 2 values correspond to the following sub-categories:
{E_vdW} = vdW (attractive) energy
{E_Rep} = Repulsive energy :ol
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
compute 0 all pair ilp/graphene/hbn
variable Evdw equal c_0\[1\]
variable Erep equal c_0\[2\]
thermo_style custom step temp epair v_Erep v_Evdw :pre
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:

18
doc/src/pair_kolmogorov_crespi_full.txt
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@ -13,7 +13,7 @@ pair_style kolmogorov/crespi/full command :h3
pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function
tap_flag = 0/1 to turn off/on the taper function :ul
[Examples:]
@ -74,6 +74,22 @@ comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the "compute
pair"_compute_pair.html command as a vector of values of length 2.
The 2 values correspond to the following sub-categories:
{E_vdW} = vdW (attractive) energy
{E_Rep} = Repulsive energy :ol
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
compute 0 all pair kolmogorov/crespi/full
variable Evdw equal c_0\[1\]
variable Erep equal c_0\[2\]
thermo_style custom step temp epair v_Erep v_Evdw :pre
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:

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examples/USER/misc/ilp_graphene_hbn/Bi_gr_AB_stack_2L_noH.data Normal file
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examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP
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@ -1 +0,0 @@
../../../../../potentials/BNCH-old.ILP

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examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH_300K.data
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examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.airebo
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@ -1 +0,0 @@
../../../../../potentials/CH.airebo

61
examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene
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@ -1,61 +0,0 @@
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
group adsorbate type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0
variable ILP equal c_1
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000

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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
680 atoms in group membrane
group adsorbate type 2
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0
variable ILP equal c_1
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564
200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465
300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539
400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113372 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709
500 -5029.3985510533 -5046.0433160610 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534
600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537
700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274644 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955
800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515
900 -5029.3930414672 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839
1000 -5029.3908907831 -5045.6437703691 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974
Loop time of 137.46 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.629 ns/day, 38.183 hours/ns, 7.275 timesteps/s
95.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 137.33 | 137.33 | 137.33 | 0.0 | 99.90
Bond | 0.00071788 | 0.00071788 | 0.00071788 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.067907 | 0.067907 | 0.067907 | 0.0 | 0.05
Output | 0.0016029 | 0.0016029 | 0.0016029 | 0.0 | 0.00
Modify | 0.036542 | 0.036542 | 0.036542 | 0.0 | 0.03
Other | | 0.02574 | | | 0.02
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 265206 ave 265206 max 265206 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 265206
Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:17

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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
680 atoms in group membrane
group adsorbate type 2
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0
variable ILP equal c_1
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564
200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465
300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539
400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113371 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709
500 -5029.3985510533 -5046.0433160611 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534
600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537
700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274643 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955
800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515
900 -5029.3930414671 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839
1000 -5029.3908907831 -5045.6437703692 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974
Loop time of 36.0917 on 4 procs for 1000 steps with 1360 atoms
Performance: 2.394 ns/day, 10.025 hours/ns, 27.707 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.204 | 34.289 | 35.893 | 17.3 | 95.01
Bond | 0.00038719 | 0.00065947 | 0.00097609 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.1539 | 1.7595 | 2.8464 | 76.7 | 4.88
Output | 0.0013447 | 0.0014529 | 0.0016887 | 0.4 | 0.00
Modify | 0.010811 | 0.012037 | 0.013764 | 1.0 | 0.03
Other | | 0.0287 | | | 0.08
Nlocal: 340 ave 344 max 334 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 4628 ave 4634 max 4624 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 66301.5 ave 67860 max 63963 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 265206
Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:36

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examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff
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../../../../../potentials/BNC.tersoff

1
examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP
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../../../../../potentials/BNCH-old.ILP

1
examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo
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../../../../../potentials/CH.airebo

71
examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN
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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
group adsorbate type 3
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2
variable Ecoul equal c_3
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000

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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
720 atoms in group membrane
group adsorbate type 3
720 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2
variable Ecoul equal c_3
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
7 neighbor lists, perpetual/occasional/extra = 6 1 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (6)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) compute group/group, occasional, copy from (7)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(7) neighbor class addition, perpetual, half/full from (6)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -10708.4531746010 -10764.2547791975 55.8016045965 -66.8250335416 -5401.7347845703 -5322.2780762734 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755
100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614
200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321
300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196
400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799
500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266
600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507737 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624
700 -10708.1867253590 -10736.6143955088 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688
800 -10708.1733385055 -10736.0277775931 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693
900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300
1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943
Loop time of 149.449 on 1 procs for 1000 steps with 1440 atoms
Performance: 0.578 ns/day, 41.514 hours/ns, 6.691 timesteps/s
96.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 149.06 | 149.06 | 149.06 | 0.0 | 99.74
Bond | 0.00082946 | 0.00082946 | 0.00082946 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.068351 | 0.068351 | 0.068351 | 0.0 | 0.05
Output | 0.25935 | 0.25935 | 0.25935 | 0.0 | 0.17
Modify | 0.030915 | 0.030915 | 0.030915 | 0.0 | 0.02
Other | | 0.02702 | | | 0.02
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8180 ave 8180 max 8180 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 140400 ave 140400 max 140400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 280800 ave 280800 max 280800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:29

171
examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4
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@ -1,171 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
720 atoms in group membrane
group adsorbate type 3
720 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2
variable Ecoul equal c_3
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
7 neighbor lists, perpetual/occasional/extra = 6 1 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (6)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) compute group/group, occasional, copy from (7)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(7) neighbor class addition, perpetual, half/full from (6)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -10708.4531746011 -10764.2547791976 55.8016045965 -66.8250335415 -5401.7347845703 -5322.2780762735 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755
100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614
200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321
300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196
400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799
500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266
600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507736 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624
700 -10708.1867253590 -10736.6143955089 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688
800 -10708.1733385055 -10736.0277775930 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693
900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300
1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943
Loop time of 39.6206 on 4 procs for 1000 steps with 1440 atoms
Performance: 2.181 ns/day, 11.006 hours/ns, 25.239 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 34.948 | 37.122 | 39.309 | 31.6 | 93.69
Bond | 0.00046444 | 0.0005914 | 0.00089121 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.20131 | 2.3895 | 4.565 | 124.7 | 6.03
Output | 0.069107 | 0.069157 | 0.069264 | 0.0 | 0.17
Modify | 0.010056 | 0.010403 | 0.010688 | 0.3 | 0.03
Other | | 0.02875 | | | 0.07
Nlocal: 360 ave 380 max 340 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4716 ave 4736 max 4696 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 35100 ave 37050 max 33150 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 70200 ave 74100 max 66300 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:39

0
examples/USER/misc/ilp_graphene_hbn/gr-hBN/gr_hBN_Cstack_2L_noH.data → examples/USER/misc/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data
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1372
examples/USER/misc/ilp_graphene_hbn/hBN_AA_prime_stack_2L_noH.data Normal file
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File diff suppressed because it is too large Load Diff

51
examples/USER/misc/ilp_graphene_hbn/in.bilayer-graphene Normal file
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@ -0,0 +1,51 @@
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
group layer2 molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0 # REBO energy
variable ILP equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000

56
examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN Normal file
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@ -0,0 +1,56 @@
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AA_prime_stack_2L_noH.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
group layer2 molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0 # Tersoff energy
variable Ecoul equal c_1 # Coulomb energy
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000

56
examples/USER/misc/ilp_graphene_hbn/in.grhBN Normal file
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@ -0,0 +1,56 @@
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer
# so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group hBN molecule 1
group gr molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
variable Ecoul equal c_3
############# Output ##############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
###### Run molecular dynamics ######
run 1000

21
examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn
View File

@ -32,14 +32,6 @@ neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
@ -51,19 +43,16 @@ compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable EILP equal c_2
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
variable ILP equal c_2
variable Evdw equal c_2[1]
variable Erep equal c_2[2]
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
thermo_modify lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes

168
examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1
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@ -1,168 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
680 atoms in group membrane
group adsorbate type 3 4
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable EILP equal c_2
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 5 1 0
(1) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (6)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) compute group/group, occasional, copy from (6)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 57.85 | 57.85 | 57.85 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801
100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275
200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807
300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614
400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122
500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319
600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794
700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989
800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553
900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606
1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557
Loop time of 202.063 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.428 ns/day, 56.129 hours/ns, 4.949 timesteps/s
91.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 201.4 | 201.4 | 201.4 | 0.0 | 99.67
Bond | 0.00092697 | 0.00092697 | 0.00092697 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.086005 | 0.086005 | 0.086005 | 0.0 | 0.04
Output | 0.50438 | 0.50438 | 0.50438 | 0.0 | 0.25
Modify | 0.038846 | 0.038846 | 0.038846 | 0.0 | 0.02
Other | | 0.03093 | | | 0.02
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7840 ave 7840 max 7840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 249628 ave 249628 max 249628 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 253390 ave 253390 max 253390 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 253390
Ave neighs/atom = 186.316
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:22

168
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
680 atoms in group membrane
group adsorbate type 3 4
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable EILP equal c_2
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 5 1 0
(1) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (6)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) compute group/group, occasional, copy from (6)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 30.63 | 30.63 | 30.64 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801
100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275
200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807
300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614
400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122
500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319
600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794
700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989
800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553
900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606
1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557
Loop time of 53.3155 on 4 procs for 1000 steps with 1360 atoms
Performance: 1.621 ns/day, 14.810 hours/ns, 18.756 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 49.475 | 50.978 | 52.988 | 18.0 | 95.62
Bond | 0.00045061 | 0.00066602 | 0.00086665 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.16491 | 2.1759 | 3.679 | 87.0 | 4.08
Output | 0.11871 | 0.11882 | 0.11911 | 0.0 | 0.22
Modify | 0.012956 | 0.013504 | 0.01387 | 0.3 | 0.03
Other | | 0.02828 | | | 0.05
Nlocal: 340 ave 346 max 336 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 4537.5 ave 4540 max 4534 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 62407 ave 62413 max 62402 min
Histogram: 1 0 0 1 1 0 0 0 0 1
FullNghs: 63347.5 ave 65585 max 61866 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 253926
Ave neighs/atom = 186.71
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:53

127
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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000290871 secs
read_data CPU = 0.00159073 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0 # REBO energy
variable ILP equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp
0 -10037.285 -10089.985 52.699361 -10057.189 -32.795185 43.640104 -76.435288 300
100 -10037.034 -10064.765 27.73131 -10032.181 -32.58421 34.730868 -67.315078 157.86516
200 -10036.963 -10061.144 24.18111 -10028.856 -32.288132 28.179936 -60.468068 137.65505
300 -10037.003 -10063.5 26.496726 -10030.823 -32.677105 34.923849 -67.600954 150.83708
400 -10037.032 -10064.389 27.356526 -10031.853 -32.535415 44.242347 -76.777762 155.73164
500 -10037.023 -10064.114 27.090279 -10031.431 -32.682418 37.229232 -69.91165 154.21598
600 -10037.003 -10063.657 26.653718 -10031.327 -32.329664 28.509073 -60.838737 151.73078
700 -10037.004 -10063.35 26.345697 -10030.801 -32.549231 32.564686 -65.113917 149.97732
800 -10037.025 -10064.219 27.194765 -10031.766 -32.453653 43.381557 -75.83521 154.81078
900 -10037.028 -10064.668 27.639127 -10032.167 -32.500121 39.99345 -72.493571 157.34039
1000 -10037.003 -10063.662 26.658825 -10031.337 -32.325053 29.573578 -61.898631 151.75986
Loop time of 149.887 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.576 ns/day, 41.635 hours/ns, 6.672 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 149.75 | 149.75 | 149.75 | 0.0 | 99.91
Bond | 0.00024772 | 0.00024772 | 0.00024772 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.086328 | 0.086328 | 0.086328 | 0.0 | 0.06
Output | 0.00036383 | 0.00036383 | 0.00036383 | 0.0 | 0.00
Modify | 0.028636 | 0.028636 | 0.028636 | 0.0 | 0.02
Other | | 0.01708 | | | 0.01
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:30

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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000157118 secs
read_data CPU = 0.00145698 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0 # REBO energy
variable ILP equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.879 | 9.879 | 9.879 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp
0 -10037.285 -10089.985 52.699361 -10057.189 -32.795185 43.640104 -76.435288 300
100 -10037.034 -10064.765 27.73131 -10032.181 -32.58421 34.730868 -67.315078 157.86516
200 -10036.963 -10061.144 24.18111 -10028.856 -32.288132 28.179936 -60.468068 137.65505
300 -10037.003 -10063.5 26.496726 -10030.823 -32.677105 34.923849 -67.600954 150.83708
400 -10037.032 -10064.389 27.356526 -10031.853 -32.535415 44.242347 -76.777762 155.73164
500 -10037.023 -10064.114 27.090279 -10031.431 -32.682418 37.229232 -69.91165 154.21598
600 -10037.003 -10063.657 26.653718 -10031.327 -32.329664 28.509073 -60.838737 151.73078
700 -10037.004 -10063.35 26.345697 -10030.801 -32.549231 32.564686 -65.113917 149.97732
800 -10037.025 -10064.219 27.194765 -10031.766 -32.453653 43.381557 -75.83521 154.81078
900 -10037.028 -10064.668 27.639127 -10032.167 -32.500121 39.99345 -72.493571 157.34039
1000 -10037.003 -10063.662 26.658825 -10031.337 -32.325053 29.573578 -61.898631 151.75986
Loop time of 44.6551 on 4 procs for 1000 steps with 1360 atoms
Performance: 1.935 ns/day, 12.404 hours/ns, 22.394 timesteps/s
93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 40.304 | 41.221 | 41.998 | 9.5 | 92.31
Bond | 0.00027633 | 0.00029379 | 0.00031424 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.5678 | 3.3334 | 4.2403 | 32.9 | 7.46
Output | 0.0051446 | 0.0054518 | 0.0059683 | 0.4 | 0.01
Modify | 0.0088317 | 0.009002 | 0.0090654 | 0.1 | 0.02
Other | | 0.08586 | | | 0.19
Nlocal: 340 ave 340 max 340 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4628 ave 4628 max 4628 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259250 ave 259250 max 259250 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:44

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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AA_prime_stack_2L_noH.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000375509 secs
read_data CPU = 0.00181293 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0 # Tersoff energy
variable Ecoul equal c_1 # Coulomb energy
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300
100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947
200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191
300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162
400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051
500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824
600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004
700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859
800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415
900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017
1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339
Loop time of 211.527 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.408 ns/day, 58.757 hours/ns, 4.728 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 211.4 | 211.4 | 211.4 | 0.0 | 99.94
Bond | 0.00018859 | 0.00018859 | 0.00018859 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.082034 | 0.082034 | 0.082034 | 0.0 | 0.04
Output | 0.00037289 | 0.00037289 | 0.00037289 | 0.0 | 0.00
Modify | 0.027928 | 0.027928 | 0.027928 | 0.0 | 0.01
Other | | 0.0159 | | | 0.01
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7836 ave 7836 max 7836 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 249560 ave 249560 max 249560 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.00504e+06 ave 1.00504e+06 max 1.00504e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1005040
Ave neighs/atom = 739
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:31

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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AA_prime_stack_2L_noH.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000224352 secs
read_data CPU = 0.00160909 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0 # Tersoff energy
variable Ecoul equal c_1 # Coulomb energy
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 18.99 | 18.99 | 18.99 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300
100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947
200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191
300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162
400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051
500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824
600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004
700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859
800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415
900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017
1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339
Loop time of 68.3631 on 4 procs for 1000 steps with 1360 atoms
Performance: 1.264 ns/day, 18.990 hours/ns, 14.628 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 64.58 | 66.38 | 67.402 | 13.2 | 97.10
Bond | 0.0001719 | 0.00021869 | 0.00024033 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.93767 | 1.9601 | 3.76 | 77.0 | 2.87
Output | 0.00033593 | 0.00061601 | 0.0014501 | 0.0 | 0.00
Modify | 0.0085733 | 0.0089303 | 0.0093236 | 0.4 | 0.01
Other | | 0.01285 | | | 0.02
Nlocal: 340 ave 340 max 340 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4536 ave 4536 max 4536 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 62390 ave 62390 max 62390 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 251260 ave 251260 max 251260 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1005040
Ave neighs/atom = 739
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:08

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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer
# so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000282049 secs
read_data CPU = 0.00159025 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group hBN molecule 1
720 atoms in group hBN
group gr molecule 2
720 atoms in group gr
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
variable Ecoul equal c_3
############# Output ##############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 22.52 | 22.52 | 22.52 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300
100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347
200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042
300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194
400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706
500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121
600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561
700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921
800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494
900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783
1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466
Loop time of 152.66 on 1 procs for 1000 steps with 1440 atoms
Performance: 0.566 ns/day, 42.406 hours/ns, 6.550 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 152.52 | 152.52 | 152.52 | 0.0 | 99.91
Bond | 0.00023174 | 0.00023174 | 0.00023174 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.087147 | 0.087147 | 0.087147 | 0.0 | 0.06
Output | 0.0004189 | 0.0004189 | 0.0004189 | 0.0 | 0.00
Modify | 0.029972 | 0.029972 | 0.029972 | 0.0 | 0.02
Other | | 0.02057 | | | 0.01
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8180 ave 8180 max 8180 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 140400 ave 140400 max 140400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 280800 ave 280800 max 280800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:32

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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer
# so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.00012207 secs
read_data CPU = 0.00357461 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group hBN molecule 1
720 atoms in group hBN
group gr molecule 2
720 atoms in group gr
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
variable Ecoul equal c_3
############# Output ##############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300
100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347
200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042
300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194
400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706
500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121
600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561
700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921
800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494
900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783
1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466
Loop time of 54.095 on 4 procs for 1000 steps with 1440 atoms
Performance: 1.597 ns/day, 15.026 hours/ns, 18.486 timesteps/s
84.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 42.138 | 45.531 | 49.106 | 42.0 | 84.17
Bond | 0.0003159 | 0.00037384 | 0.000489 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 4.71 | 8.2803 | 11.682 | 98.3 | 15.31
Output | 0.0021999 | 0.0055975 | 0.013382 | 6.0 | 0.01
Modify | 0.0092845 | 0.010981 | 0.012538 | 1.3 | 0.02
Other | | 0.2673 | | | 0.49
Nlocal: 360 ave 380 max 340 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4716 ave 4736 max 4696 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 35100 ave 37050 max 33150 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 70200 ave 74100 max 66300 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:54

154
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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000251532 secs
read_data CPU = 0.00451231 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
680 atoms in group membrane
group adsorbate type 3 4
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable ILP equal c_2
variable Evdw equal c_2[1]
variable Erep equal c_2[2]
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
thermo_modify lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair tersoff, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual, half/full from (4)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 54.59 | 54.59 | 54.59 Mbytes
Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp
0 -5114.6628 -5127.8586 13.195828 -5091.4121 -36.083114 -0.36343598 38.918674 -75.001787 75.119474
100 -5114.6621 -5127.6958 13.033777 -5091.2408 -36.09276 -0.36228286 38.769906 -74.862666 74.196973
200 -5114.6631 -5127.5945 12.93145 -5091.1508 -36.086669 -0.35708801 38.20076 -74.287429 73.614462
300 -5114.6694 -5128.3286 13.65924 -5091.8646 -36.110786 -0.35328159 37.758284 -73.86907 77.757528
400 -5114.6614 -5127.6424 12.980975 -5091.2348 -36.049634 -0.35794328 38.247252 -74.296886 73.896389
500 -5114.66 -5127.4098 12.749794 -5090.9285 -36.119571 -0.36174976 38.745548 -74.865119 72.580351
600 -5114.6673 -5128.0913 13.424021 -5091.6339 -36.09384 -0.36356991 38.927401 -75.021241 76.418503
700 -5114.661 -5127.7467 13.085707 -5091.2811 -36.106639 -0.35892399 38.332616 -74.439255 74.492596
800 -5114.6623 -5128.013 13.350778 -5091.5694 -36.089718 -0.35392503 37.851602 -73.94132 76.001554
900 -5114.6675 -5128.1497 13.482146 -5091.6704 -36.124679 -0.35462869 37.885183 -74.009861 76.749392
1000 -5114.6683 -5128.3365 13.668146 -5091.937 -36.037596 -0.36184347 38.709718 -74.747314 77.808228
Loop time of 207.028 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.417 ns/day, 57.508 hours/ns, 4.830 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 206.9 | 206.9 | 206.9 | 0.0 | 99.94
Bond | 0.00019169 | 0.00019169 | 0.00019169 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.081397 | 0.081397 | 0.081397 | 0.0 | 0.04
Output | 0.00036597 | 0.00036597 | 0.00036597 | 0.0 | 0.00
Modify | 0.033408 | 0.033408 | 0.033408 | 0.0 | 0.02
Other | | 0.01615 | | | 0.01
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7840 ave 7840 max 7840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 249628 ave 249628 max 249628 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 253390 ave 253390 max 253390 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 253390
Ave neighs/atom = 186.316
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:27

154
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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000332117 secs
read_data CPU = 0.00270581 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
680 atoms in group membrane
group adsorbate type 3 4
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable ILP equal c_2
variable Evdw equal c_2[1]
variable Erep equal c_2[2]
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
thermo_modify lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair tersoff, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual, half/full from (4)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 28.9 | 28.9 | 28.9 Mbytes
Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp
0 -5114.6628 -5127.8586 13.195828 -5091.4121 -36.083114 -0.36343598 38.918674 -75.001787 75.119474
100 -5114.6621 -5127.6958 13.033777 -5091.2408 -36.09276 -0.36228286 38.769906 -74.862666 74.196973
200 -5114.6631 -5127.5945 12.93145 -5091.1508 -36.086669 -0.35708801 38.20076 -74.287429 73.614462
300 -5114.6694 -5128.3286 13.65924 -5091.8646 -36.110786 -0.35328159 37.758284 -73.86907 77.757528
400 -5114.6614 -5127.6424 12.980975 -5091.2348 -36.049634 -0.35794328 38.247252 -74.296886 73.896389
500 -5114.66 -5127.4098 12.749794 -5090.9285 -36.119571 -0.36174976 38.745548 -74.865119 72.580351
600 -5114.6673 -5128.0913 13.424021 -5091.6339 -36.09384 -0.36356991 38.927401 -75.021241 76.418503
700 -5114.661 -5127.7467 13.085707 -5091.2811 -36.106639 -0.35892399 38.332616 -74.439255 74.492596
800 -5114.6623 -5128.013 13.350778 -5091.5694 -36.089718 -0.35392503 37.851602 -73.94132 76.001554
900 -5114.6675 -5128.1497 13.482146 -5091.6704 -36.124679 -0.35462869 37.885183 -74.009861 76.749392
1000 -5114.6683 -5128.3365 13.668146 -5091.937 -36.037596 -0.36184347 38.709718 -74.747314 77.808228
Loop time of 65.9005 on 4 procs for 1000 steps with 1360 atoms
Performance: 1.311 ns/day, 18.306 hours/ns, 15.174 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 63.244 | 64.208 | 65.281 | 10.1 | 97.43
Bond | 0.00013971 | 0.00017679 | 0.00022101 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.58237 | 1.6612 | 2.6292 | 63.1 | 2.52
Output | 0.0003171 | 0.00062358 | 0.0015192 | 0.0 | 0.00
Modify | 0.010251 | 0.010509 | 0.01075 | 0.2 | 0.02
Other | | 0.02025 | | | 0.03
Nlocal: 340 ave 346 max 336 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 4537.5 ave 4540 max 4534 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 62407 ave 62413 max 62402 min
Histogram: 1 0 0 1 1 0 0 0 0 1
FullNghs: 63347.5 ave 65585 max 61866 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 253926
Ave neighs/atom = 186.71
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:06

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examples/USER/misc/kolmogorov_crespi_full/CH.KC Symbolic link
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../../../../potentials/CH.KC

1
examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC Symbolic link
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../../../../potentials/CH_taper.KC

52
examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene
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@ -5,21 +5,22 @@ atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
read_data Bi_gr_AB_stack_2L_noH.data
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
group adsorbate type 2
group layer1 molecule 1
group layer2 molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
####################################################################
pair_coeff * * rebo CH.rebo NULL C # chemical
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
pair_coeff * * rebo CH.rebo C C # chemical
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
@ -27,34 +28,25 @@ neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair kolmogorov/crespi/full
variable REBO equal c_0
variable KC equal c_1
compute 0 all pair rebo
compute 1 all pair kolmogorov/crespi/full
variable REBO equal c_0 # REBO energy
variable KC equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
###### Run molecular dynamics ######
run 1000
fix thermostat all nve
run 1000

129
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LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000143357 secs
read_data CPU = 0.00128686 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair kolmogorov/crespi/full
variable REBO equal c_0 # REBO energy
variable KC equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair kolmogorov/crespi/full, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp
0 0.0000000000000000 -10037.7640583248121402 -10090.4634194413119985 52.6993611164999436 -10057.1894932863488066 -33.2739261549639664 35.9559834316876348 -69.2299095866357561 299.9999999999996589
100 5.3877589240437374 -10037.5122858156355505 -10065.4637593850693520 27.9514735694345475 -10032.2132655062632693 -33.2504938788055995 25.2100699045900747 -58.4605637833913789 159.1184768311149185
200 10.7755050340201706 -10037.4414086674350983 -10061.6271012692632212 24.1856926018286202 -10028.9093252939674130 -32.7177759752951403 18.5366534598604176 -51.2544294351563394 137.6811336385792970
300 16.1665089030284435 -10037.4824653300311184 -10064.2845326005663082 26.8020672705344225 -10030.9195389405322203 -33.3649936600345924 26.3639208740001152 -59.7289145340284122 152.5752876469470891
400 21.5454839280573651 -10037.5105626329259394 -10064.8769084956420556 27.3663458627154164 -10031.8478821022799821 -33.0290263933626349 36.6142885774199272 -69.6433149707719963 155.7875386888538571
500 26.9370588400634006 -10037.5010433785082569 -10064.8363209936451312 27.3352776151367571 -10031.4417172103931080 -33.3946037832518243 26.2980262321670750 -59.6926300154142595 155.6106774503846850
600 32.4204196080099791 -10037.4817772372425679 -10064.1925798287738871 26.7108025915316247 -10031.4376178099264507 -32.7549620188478201 18.5745873777024606 -51.3295493965519327 152.0557480714992380
700 37.8001567909959704 -10037.4834430268438155 -10064.1291975032218033 26.6457544763788299 -10030.8722888097800023 -33.2569086934421492 25.2322818106646771 -58.4891905041015008 151.6854507067418467
800 43.1622281169984490 -10037.5047888097760733 -10064.8671187128948077 27.3623299031188978 -10031.9815058608437539 -32.8856128520517217 36.5236695083771536 -69.4092823604148350 155.7646771616279011
900 48.5261204120470211 -10037.5068323940176924 -10065.3998155271074211 27.8929831330889542 -10032.1734374829957233 -33.2263780441125931 27.7314849391008309 -60.9578629832065317 158.7855101588076820
1000 53.8888844919856638 -10037.4811494880468672 -10064.0099109142265661 26.5287614261789670 -10031.3325267421259923 -32.6773841721003464 18.9005970229871600 -51.5779811950879434 151.0194480396057202
Loop time of 53.8889 on 1 procs for 1000 steps with 1360 atoms
Performance: 1.603 ns/day, 14.969 hours/ns, 18.557 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 53.836 | 53.836 | 53.836 | 0.0 | 99.90
Bond | 0.00043479 | 0.00043479 | 0.00043479 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.032452 | 0.032452 | 0.032452 | 0.0 | 0.06
Output | 0.00058326 | 0.00058326 | 0.00058326 | 0.0 | 0.00
Modify | 0.0094135 | 0.0094135 | 0.0094135 | 0.0 | 0.02
Other | | 0.009815 | | | 0.02
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:54

129
examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.4 Normal file
View File

@ -0,0 +1,129 @@
LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000245051 secs
read_data CPU = 0.00257704 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair kolmogorov/crespi/full
variable REBO equal c_0 # REBO energy
variable KC equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair kolmogorov/crespi/full, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.878 | 9.878 | 9.878 Mbytes
Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp
0 0.0000000000000000 -10037.7640583250176860 -10090.4634194415175443 52.6993611164999933 -10057.1894932866325689 -33.2739261548851388 35.9559834317043467 -69.2299095866038954 299.9999999999999432
100 1.5180600649910048 -10037.5122858156355505 -10065.4637593850711710 27.9514735694348637 -10032.2132655062741833 -33.2504938787968172 25.2100699046001573 -58.4605637833912795 159.1184768311167090
200 3.0089348420733586 -10037.4414086674296414 -10061.6271012692577642 24.1856926018279914 -10028.9093252939601371 -32.7177759752976272 18.5366534598677504 -51.2544294351567515 137.6811336385757158
300 4.5315427089808509 -10037.4824653300020145 -10064.2845326005372044 26.8020672705348311 -10030.9195389405158494 -33.3649936600211205 26.3639208740115549 -59.7289145340278722 152.5752876469494197
400 6.0353655620710924 -10037.5105626329095685 -10064.8769084956238657 27.3663458627148124 -10031.8478821022818011 -33.0290263933414394 36.6142885774347562 -69.6433149707726074 155.7875386888504181
500 7.5396006110822782 -10037.5010433784900670 -10064.8363209936269413 27.3352776151361780 -10031.4417172103858320 -33.3946037832416351 26.2980262321774489 -59.6926300154146787 155.6106774503813881
600 9.2617433650884777 -10037.4817772372534819 -10064.1925798287848011 26.7108025915320830 -10031.4376178099319077 -32.7549620188514226 18.5745873777100208 -51.3295493965524017 152.0557480715018528
700 10.7484918619738892 -10037.4834430268347205 -10064.1291975032127084 26.6457544763787268 -10030.8722888097836403 -33.2569086934306739 25.2322818106757047 -58.4891905041008613 151.6854507067412499
800 12.2509897360578179 -10037.5047888097869873 -10064.8671187129039026 27.3623299031166667 -10031.9815058608728577 -32.8856128520297801 36.5236695083899718 -69.4092823604150908 155.7646771616151966
900 13.7584852169966325 -10037.5068323939758557 -10065.3998155270637653 27.8929831330881477 -10032.1734374829648004 -33.2263780440982259 27.7314849391120788 -60.9578629832060841 158.7855101588031062
1000 15.2755981830414385 -10037.4811494880432292 -10064.0099109142211091 26.5287614261777058 -10031.3325267421205353 -32.6773841721017888 18.9005970229946634 -51.5779811950868776 151.0194480395985295
Loop time of 15.2757 on 4 procs for 1000 steps with 1360 atoms
Performance: 5.656 ns/day, 4.243 hours/ns, 65.464 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.985 | 14.446 | 14.823 | 7.9 | 94.57
Bond | 0.00040979 | 0.00042456 | 0.00046059 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.43692 | 0.81428 | 1.2749 | 33.2 | 5.33
Output | 0.00028016 | 0.00037143 | 0.00063561 | 0.0 | 0.00
Modify | 0.0045586 | 0.0046468 | 0.0047903 | 0.1 | 0.03
Other | | 0.01041 | | | 0.07
Nlocal: 340 ave 340 max 340 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4628 ave 4628 max 4628 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259250 ave 259250 max 259250 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:15

1
lib/colvars/Makefile.common
View File

@ -34,6 +34,7 @@ COLVARS_SRCS = \
colvarcomp_coordnums.cpp \
colvarcomp.cpp \
colvarcomp_distances.cpp \
colvarcomp_gpath.cpp \
colvarcomp_protein.cpp \
colvarcomp_rotations.cpp \
colvar.cpp \

20
lib/colvars/colvar.cpp
View File

@ -791,6 +791,11 @@ int colvar::init_components(std::string const &conf)
"inertia", "inertia");
error_code |= init_components_type<inertia_z>(conf, "moment of inertia around an axis", "inertiaZ");
error_code |= init_components_type<eigenvector>(conf, "eigenvector", "eigenvector");
error_code |= init_components_type<gspath>(conf, "geometrical path collective variables (s)", "gspath");
error_code |= init_components_type<gzpath>(conf, "geometrical path collective variables (z)", "gzpath");
error_code |= init_components_type<linearCombination>(conf, "linear combination of other collective variables", "subColvar");
error_code |= init_components_type<gspathCV>(conf, "geometrical path collective variables (s) for other CVs", "gspathCV");
error_code |= init_components_type<gzpathCV>(conf, "geometrical path collective variables (z) for other CVs", "gzpathCV");
if (!cvcs.size() || (error_code != COLVARS_OK)) {
cvm::error("Error: no valid components were provided "
@ -1495,6 +1500,8 @@ int colvar::calc_colvar_properties()
// calculate the velocity by finite differences
if (cvm::step_relative() == 0) {
x_old = x;
v_fdiff.reset(); // Do not pretend we know anything about the actual velocity
// eg. upon restarting. That would require saving v_fdiff or x_old to the state file
} else {
v_fdiff = fdiff_velocity(x_old, x);
v_reported = v_fdiff;
@ -1516,8 +1523,9 @@ int colvar::calc_colvar_properties()
x_ext = prev_x_ext;
v_ext = prev_v_ext;
}
// report the restraint center as "value"
// These position and velocities come from integration at the _previous timestep_ in update_forces_energy()
// But we report values at the beginning of the timestep (value at t=0 on the first timestep)
x_reported = x_ext;
v_reported = v_ext;
// the "total force" with the extended Lagrangian is
@ -1651,8 +1659,6 @@ cvm::real colvar::update_forces_energy()
// is equal to the actual coordinate
x_ext = x;
}
// Report extended value
x_reported = x_ext;
}
// Now adding the force on the actual colvar (for those biases that
@ -1975,9 +1981,8 @@ std::istream & colvar::read_restart(std::istream &is)
}
if (is_enabled(f_cv_extended_Lagrangian)) {
if ( !(get_keyval(conf, "extended_x", x_ext,
colvarvalue(x.type()), colvarparse::parse_silent)) &&
colvarvalue(x.type()), colvarparse::parse_silent)) ||
!(get_keyval(conf, "extended_v", v_ext,
colvarvalue(x.type()), colvarparse::parse_silent)) ) {
cvm::log("Error: restart file does not contain "
@ -2079,11 +2084,11 @@ std::ostream & colvar::write_restart(std::ostream &os) {
os << " extended_x "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< x_ext << "\n"
<< x_reported << "\n"
<< " extended_v "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< v_ext << "\n";
<< v_reported << "\n";
}
os << "}\n\n";
@ -2150,7 +2155,6 @@ std::ostream & colvar::write_traj_label(std::ostream & os)
std::ostream & colvar::write_traj(std::ostream &os)
{
os << " ";
if (is_enabled(f_cv_output_value)) {
if (is_enabled(f_cv_extended_Lagrangian)) {

8
lib/colvars/colvar.h
View File

@ -569,6 +569,14 @@ public:
class alpha_dihedrals;
class alpha_angles;
class dihedPC;
class componentDisabled;
class CartesianBasedPath;
class gspath;
class gzpath;
class linearCombination;
class CVBasedPath;
class gspathCV;
class gzpathCV;
// non-scalar components
class distance_vec;

270
lib/colvars/colvar_geometricpath.h Normal file
View File

@ -0,0 +1,270 @@
#ifndef GEOMETRICPATHCV_H
#define GEOMETRICPATHCV_H
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <vector>
#include <cmath>
#include <iostream>
#include <algorithm>
#include <string>
#include <map>
namespace GeometricPathCV {
enum path_sz {S, Z};
template <typename element_type, typename scalar_type, path_sz path_type>
class GeometricPathBase {
private:
struct doCompareFrameDistance {
doCompareFrameDistance(const GeometricPathBase& obj): m_obj(obj) {}
const GeometricPathBase& m_obj;
bool operator()(const size_t& i1, const size_t& i2) {
return m_obj.frame_distances[i1] < m_obj.frame_distances[i2];
}
};
protected:
scalar_type v1v1;
scalar_type v2v2;
scalar_type v3v3;
scalar_type v4v4;
scalar_type v1v3;
scalar_type v1v4;
scalar_type f;
scalar_type dx;
scalar_type s;
scalar_type z;
scalar_type zz;
std::vector<element_type> v1;
std::vector<element_type> v2;
std::vector<element_type> v3;
std::vector<element_type> v4;
std::vector<element_type> dfdv1;
std::vector<element_type> dfdv2;
std::vector<element_type> dzdv1;
std::vector<element_type> dzdv2;
std::vector<scalar_type> frame_distances;
std::vector<size_t> frame_index;
bool use_second_closest_frame;
bool use_third_closest_frame;
bool use_z_square;
long min_frame_index_1;
long min_frame_index_2;
long min_frame_index_3;
long sign;
double M;
double m;
public:
GeometricPathBase(size_t vector_size, const element_type& element = element_type(), size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
GeometricPathBase(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
GeometricPathBase() {}
virtual ~GeometricPathBase() {}
virtual void initialize(size_t vector_size, const element_type& element = element_type(), size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
virtual void initialize(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
virtual void prepareVectors();
virtual void updateReferenceDistances();
virtual void compute();
virtual void determineClosestFrames();
virtual void computeValue();
virtual void computeDerivatives();
};
template <typename element_type, typename scalar_type, path_sz path_type>
GeometricPathBase<element_type, scalar_type, path_type>::GeometricPathBase(size_t vector_size, const element_type& element, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
initialize(vector_size, element, total_frames, p_use_second_closest_frame, p_use_third_closest_frame, p_use_z_square);
}
template <typename element_type, typename scalar_type, path_sz path_type>
GeometricPathBase<element_type, scalar_type, path_type>::GeometricPathBase(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
initialize(vector_size, elements, total_frames, p_use_second_closest_frame, p_use_third_closest_frame, p_use_z_square);
}
template <typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t vector_size, const element_type& element, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
v1v1 = scalar_type();
v2v2 = scalar_type();
v3v3 = scalar_type();
v4v4 = scalar_type();
v1v3 = scalar_type();
v1v4 = scalar_type();
f = scalar_type();
dx = scalar_type();
z = scalar_type();
zz = scalar_type();
sign = 0;
v1.resize(vector_size, element);
v2.resize(vector_size, element);
v3.resize(vector_size, element);
v4.resize(vector_size, element);
dfdv1.resize(vector_size, element);
dfdv2.resize(vector_size, element);
dzdv1.resize(vector_size, element);
dzdv2.resize(vector_size, element);
frame_distances.resize(total_frames);
frame_index.resize(total_frames);
for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
frame_index[i_frame] = i_frame;
}
use_second_closest_frame = p_use_second_closest_frame;
use_third_closest_frame = p_use_third_closest_frame;
use_z_square = p_use_z_square;
M = static_cast<scalar_type>(total_frames - 1);
m = static_cast<scalar_type>(1.0);
}
template <typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
v1v1 = scalar_type();
v2v2 = scalar_type();
v3v3 = scalar_type();
v4v4 = scalar_type();
v1v3 = scalar_type();
v1v4 = scalar_type();
f = scalar_type();
dx = scalar_type();
z = scalar_type();
zz = scalar_type();
sign = 0;
v1 = elements;
v2 = elements;
v3 = elements;
v4 = elements;
dfdv1 = elements;
dfdv2 = elements;
dzdv1 = elements;
dzdv2 = elements;
frame_distances.resize(total_frames);
frame_index.resize(total_frames);
for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
frame_index[i_frame] = i_frame;
}
use_second_closest_frame = p_use_second_closest_frame;
use_third_closest_frame = p_use_third_closest_frame;
use_z_square = p_use_z_square;
M = static_cast<scalar_type>(total_frames - 1);
m = static_cast<scalar_type>(1.0);
}
template <typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathBase<element_type, scalar_type, path_type>::prepareVectors() {
std::cout << "Warning: you should not call the prepareVectors() in base class!\n";
std::cout << std::flush;
}
template <typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathBase<element_type, scalar_type, path_type>::updateReferenceDistances() {
std::cout << "Warning: you should not call the updateReferenceDistances() in base class!\n";
std::cout << std::flush;
}
template <typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathBase<element_type, scalar_type, path_type>::compute() {
computeValue();
computeDerivatives();
}
template <typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathBase<element_type, scalar_type, path_type>::determineClosestFrames() {
// Find the closest and the second closest frames
std::sort(frame_index.begin(), frame_index.end(), doCompareFrameDistance(*this));
// Determine the sign
sign = static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1]);
if (sign > 1) {
// sigma(z) is on the left side of the closest frame
sign = 1;
} else if (sign < -1) {
// sigma(z) is on the right side of the closest frame
sign = -1;
}
if (std::abs(static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1])) > 1) {
std::cout << "Warning: Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame\n";
std::cout << " Please check your configuration or increase restraint on z(σ)\n";
for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
std::cout << "Frame index: " << frame_index[i_frame] << " ; optimal RMSD = " << frame_distances[frame_index[i_frame]] << "\n";
}
}
min_frame_index_1 = frame_index[0]; // s_m
min_frame_index_2 = use_second_closest_frame ? frame_index[1] : min_frame_index_1 - sign; // s_(m-1)
min_frame_index_3 = use_third_closest_frame ? frame_index[2] : min_frame_index_1 + sign; // s_(m+1)
m = static_cast<double>(frame_index[0]);
}
template <typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathBase<element_type, scalar_type, path_type>::computeValue() {
updateReferenceDistances();
determineClosestFrames();
prepareVectors();
v1v1 = scalar_type();
v2v2 = scalar_type();
v3v3 = scalar_type();
v1v3 = scalar_type();
if (path_type == Z) {
v1v4 = scalar_type();
v4v4 = scalar_type();
}
for (size_t i_elem = 0; i_elem < v1.size(); ++i_elem) {
v1v1 += v1[i_elem] * v1[i_elem];
v2v2 += v2[i_elem] * v2[i_elem];
v3v3 += v3[i_elem] * v3[i_elem];
v1v3 += v1[i_elem] * v3[i_elem];
if (path_type == Z) {
v1v4 += v1[i_elem] * v4[i_elem];
v4v4 += v4[i_elem] * v4[i_elem];
}
}
f = (std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)) - v1v3) / v3v3;
if (path_type == Z) {
dx = 0.5 * (f - 1);
zz = v1v1 + 2 * dx * v1v4 + dx * dx * v4v4;
if (use_z_square) {
z = zz;
} else {
z = std::sqrt(std::fabs(zz));
}
}
if (path_type == S) {
s = m/M + static_cast<double>(sign) * ((f - 1) / (2 * M));
}
}
template <typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathBase<element_type, scalar_type, path_type>::computeDerivatives() {
const scalar_type factor1 = 1.0 / (2.0 * v3v3 * std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)));
const scalar_type factor2 = 1.0 / v3v3;
for (size_t i_elem = 0; i_elem < v1.size(); ++i_elem) {
// Compute the derivative of f with vector v1
dfdv1[i_elem] = factor1 * (2.0 * v1v3 * v3[i_elem] - 2.0 * v3v3 * v1[i_elem]) - factor2 * v3[i_elem];
// Compute the derivative of f with respect to vector v2
dfdv2[i_elem] = factor1 * (2.0 * v3v3 * v2[i_elem]);
// dZ(v1(r), v2(r), v3) / dr = ∂Z/∂v1 * dv1/dr + ∂Z/∂v2 * dv2/dr
// dv1/dr = [fitting matrix 1][-1, ..., -1]
// dv2/dr = [fitting matrix 2][1, ..., 1]
// ∂Z/∂v1 = 1/(2*z) * (2v1 + (f-1)v4 + (v1⋅v4)∂f/∂v1 + v4^2 * 1/4 * 2(f-1) * ∂f/∂v1)
// ∂Z/∂v2 = 1/(2*z) * ((v1⋅v4)∂f/∂v2 + v4^2 * 1/4 * 2(f-1) * ∂f/∂v2)
if (path_type == Z) {
if (use_z_square) {
dzdv1[i_elem] = 2.0 * v1[i_elem] + (f-1) * v4[i_elem] + v1v4 * dfdv1[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv1[i_elem];
dzdv2[i_elem] = v1v4 * dfdv2[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv2[i_elem];
} else {
if (z > static_cast<scalar_type>(0)) {
dzdv1[i_elem] = (1.0 / (2.0 * z)) * (2.0 * v1[i_elem] + (f-1) * v4[i_elem] + v1v4 * dfdv1[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv1[i_elem]);
dzdv2[i_elem] = (1.0 / (2.0 * z)) * (v1v4 * dfdv2[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv2[i_elem]);
} else {
// workaround at z = 0
dzdv1[i_elem] = 0;
dzdv2[i_elem] = 0;
}
}
}
}
}
}
#endif // GEOMETRICPATHCV_H

202
lib/colvars/colvarbias_meta.cpp
View File

@ -37,7 +37,6 @@ colvarbias_meta::colvarbias_meta(char const *key)
{
new_hills_begin = hills.end();
hills_traj_os = NULL;
replica_hills_os = NULL;
ebmeta_equil_steps = 0L;
}
@ -203,23 +202,37 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
target_dist = new colvar_grid_scalar();
target_dist->init_from_colvars(colvars);
std::string target_dist_file;
get_keyval(conf, "targetdistfile", target_dist_file);
get_keyval(conf, "targetDistFile", target_dist_file);
std::ifstream targetdiststream(target_dist_file.c_str());
target_dist->read_multicol(targetdiststream);
cvm::real min_val = target_dist->minimum_value();
cvm::real max_val = target_dist->maximum_value();
if(min_val<0){
cvm::error("Error: Target distribution of ebMeta "
cvm::error("Error: Target distribution of EBMetaD "
"has negative values!.\n", INPUT_ERROR);
}
cvm::real min_pos_val = target_dist->minimum_pos_value();
if(min_pos_val<=0){
cvm::error("Error: Target distribution of ebMeta has negative "
"or zero minimum positive value!.\n", INPUT_ERROR);
}
if(min_val==0){
cvm::log("WARNING: Target distribution has zero values.\n");
cvm::log("Zeros will be converted to the minimum positive value.\n");
target_dist->remove_zeros(min_pos_val);
cvm::real target_dist_min_val;
get_keyval(conf, "targetDistMinVal", target_dist_min_val, 1/1000000.0);
if(target_dist_min_val>0 && target_dist_min_val<1){
target_dist_min_val=max_val*target_dist_min_val;
target_dist->remove_small_values(target_dist_min_val);
} else {
if (target_dist_min_val==0) {
cvm::log("NOTE: targetDistMinVal is set to zero, the minimum value of the target \n");
cvm::log(" distribution will be set as the minimum positive value.\n");
cvm::real min_pos_val = target_dist->minimum_pos_value();
if(min_pos_val<=0){
cvm::error("Error: Target distribution of EBMetaD has negative "
"or zero minimum positive value!.\n", INPUT_ERROR);
}
if(min_val==0){
cvm::log("WARNING: Target distribution has zero values.\n");
cvm::log("Zeros will be converted to the minimum positive value.\n");
target_dist->remove_small_values(min_pos_val);
}
} else {
cvm::error("Error: targetDistMinVal must be a value between 0 and 1!.\n", INPUT_ERROR);
}
}
// normalize target distribution and multiply by effective volume = exp(differential entropy)
target_dist->multiply_constant(1.0/target_dist->integral());
@ -235,14 +248,14 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
colvarbias_meta::~colvarbias_meta()
{
colvarbias_meta::clear_state_data();
colvarproxy *proxy = cvm::proxy;
if (replica_hills_os) {
cvm::proxy->close_output_stream(replica_hills_file);
replica_hills_os = NULL;
if (proxy->get_output_stream(replica_hills_file)) {
proxy->close_output_stream(replica_hills_file);
}
if (hills_traj_os) {
cvm::proxy->close_output_stream(hills_traj_file_name());
proxy->close_output_stream(hills_traj_file_name());
hills_traj_os = NULL;
}
@ -523,6 +536,8 @@ int colvarbias_meta::update_bias()
case multiple_replicas:
create_hill(hill(hill_weight*hills_scale, colvars, hill_width, replica_id));
std::ostream *replica_hills_os =
cvm::proxy->get_output_stream(replica_hills_file);
if (replica_hills_os) {
*replica_hills_os << hills.back();
} else {
@ -921,13 +936,16 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter h_first
int colvarbias_meta::replica_share()
{
colvarproxy *proxy = cvm::proxy;
// sync with the other replicas (if needed)
if (comm == multiple_replicas) {
// reread the replicas registry
update_replicas_registry();
// empty the output buffer
std::ostream *replica_hills_os =
proxy->get_output_stream(replica_hills_file);
if (replica_hills_os) {
cvm::proxy->flush_output_stream(replica_hills_os);
proxy->flush_output_stream(replica_hills_os);
}
read_replica_files();
}
@ -1089,11 +1107,7 @@ void colvarbias_meta::read_replica_files()
(replicas[ir])->replica_state_file+"\".\n");
std::ifstream is((replicas[ir])->replica_state_file.c_str());
if (! (replicas[ir])->read_state(is)) {
cvm::log("Reading from file \""+(replicas[ir])->replica_state_file+
"\" failed or incomplete: will try again in "+
cvm::to_str(replica_update_freq)+" steps.\n");
} else {
if ((replicas[ir])->read_state(is)) {
// state file has been read successfully
(replicas[ir])->replica_state_file_in_sync = true;
(replicas[ir])->update_status = 0;
@ -1550,15 +1564,11 @@ int colvarbias_meta::setup_output()
// for the others to read
// open the "hills" buffer file
if (!replica_hills_os) {
cvm::proxy->backup_file(replica_hills_file);
replica_hills_os = cvm::proxy->output_stream(replica_hills_file);
if (!replica_hills_os) return cvm::get_error();
replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
}
reopen_replica_buffer_file();
// write the state file (so that there is always one available)
write_replica_state_file();
// schedule to read the state files of the other replicas
for (size_t ir = 0; ir < replicas.size(); ir++) {
(replicas[ir])->replica_state_file_in_sync = false;
@ -1661,15 +1671,16 @@ std::ostream & colvarbias_meta::write_state_data(std::ostream& os)
int colvarbias_meta::write_state_to_replicas()
{
int error_code = COLVARS_OK;
if (comm != single_replica) {
write_replica_state_file();
// schedule to reread the state files of the other replicas (they
// have also rewritten them)
error_code |= write_replica_state_file();
error_code |= reopen_replica_buffer_file();
// schedule to reread the state files of the other replicas
for (size_t ir = 0; ir < replicas.size(); ir++) {
(replicas[ir])->replica_state_file_in_sync = false;
}
}
return COLVARS_OK;
return error_code;
}
@ -1693,6 +1704,20 @@ void colvarbias_meta::write_pmf()
// output the PMF from this instance or replica
pmf->reset();
pmf->add_grid(*hills_energy);
if (ebmeta) {
int nt_points=pmf->number_of_points();
for (int i = 0; i < nt_points; i++) {
cvm:: real pmf_val=0.0;
cvm:: real target_val=target_dist->value(i);
if (target_val>0) {
pmf_val=pmf->value(i);
pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val);
}
pmf->set_value(i,pmf_val);
}
}
cvm::real const max = pmf->maximum_value();
pmf->add_constant(-1.0 * max);
pmf->multiply_constant(-1.0);
@ -1716,10 +1741,24 @@ void colvarbias_meta::write_pmf()
if (comm != single_replica) {
// output the combined PMF from all replicas
pmf->reset();
pmf->add_grid(*hills_energy);
// current replica already included in the pools of replicas
for (size_t ir = 0; ir < replicas.size(); ir++) {
pmf->add_grid(*(replicas[ir]->hills_energy));
}
if (ebmeta) {
int nt_points=pmf->number_of_points();
for (int i = 0; i < nt_points; i++) {
cvm:: real pmf_val=0.0;
cvm:: real target_val=target_dist->value(i);
if (target_val>0) {
pmf_val=pmf->value(i);
pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val);
}
pmf->set_value(i,pmf_val);
}
}
cvm::real const max = pmf->maximum_value();
pmf->add_constant(-1.0 * max);
pmf->multiply_constant(-1.0);
@ -1744,74 +1783,47 @@ void colvarbias_meta::write_pmf()
int colvarbias_meta::write_replica_state_file()
{
colvarproxy *proxy = cvm::proxy;
if (cvm::debug()) {
cvm::log("Writing replica state file for bias \""+name+"\"\n");
}
// write down also the restart for the other replicas
cvm::backup_file(replica_state_file.c_str());
std::ostream *rep_state_os = cvm::proxy->output_stream(replica_state_file);
if (rep_state_os == NULL) {
cvm::error("Error: in opening file \""+
replica_state_file+"\" for writing.\n", FILE_ERROR);
return FILE_ERROR;
int error_code = COLVARS_OK;
// Write to temporary state file
std::string const tmp_state_file(replica_state_file+".tmp");
error_code |= proxy->remove_file(tmp_state_file);
std::ostream *rep_state_os = cvm::proxy->output_stream(tmp_state_file);
if (rep_state_os) {
if (!write_state(*rep_state_os)) {
error_code |= cvm::error("Error: in writing to temporary file \""+
tmp_state_file+"\".\n", FILE_ERROR);
}
}
error_code |= proxy->close_output_stream(tmp_state_file);
rep_state_os->setf(std::ios::scientific, std::ios::floatfield);
error_code |= proxy->rename_file(tmp_state_file, replica_state_file);
if (!write_state(*rep_state_os)) {
cvm::error("Error: in writing to file \""+
replica_state_file+"\".\n", FILE_ERROR);
cvm::proxy->close_output_stream(replica_state_file);
return FILE_ERROR;
return error_code;
}
int colvarbias_meta::reopen_replica_buffer_file()
{
int error_code = COLVARS_OK;
colvarproxy *proxy = cvm::proxy;
if (proxy->get_output_stream(replica_hills_file) != NULL) {
error_code |= proxy->close_output_stream(replica_hills_file);
}
cvm::proxy->close_output_stream(replica_state_file);
// rep_state_os.setf(std::ios::scientific, std::ios::floatfield);
// rep_state_os << "\n"
// << "metadynamics {\n"
// << " configuration {\n"
// << " name " << this->name << "\n"
// << " step " << cvm::step_absolute() << "\n";
// if (this->comm != single_replica) {
// rep_state_os << " replicaID " << this->replica_id << "\n";
// }
// rep_state_os << " }\n\n";
// rep_state_os << " hills_energy\n";
// rep_state_os << std::setprecision(cvm::cv_prec)
// << std::setw(cvm::cv_width);
// hills_energy->write_restart(rep_state_os);
// rep_state_os << " hills_energy_gradients\n";
// rep_state_os << std::setprecision(cvm::cv_prec)
// << std::setw(cvm::cv_width);
// hills_energy_gradients->write_restart(rep_state_os);
// if ( (!use_grids) || keep_hills ) {
// // write all hills currently in memory
// for (std::list<hill>::const_iterator h = this->hills.begin();
// h != this->hills.end();
// h++) {
// rep_state_os << *h;
// }
// } else {
// // write just those that are near the grid boundaries
// for (std::list<hill>::const_iterator h = this->hills_off_grid.begin();
// h != this->hills_off_grid.end();
// h++) {
// rep_state_os << *h;
// }
// }
// rep_state_os << "}\n\n";
// rep_state_os.close();
// reopen the hills file
cvm::proxy->close_output_stream(replica_hills_file);
cvm::proxy->backup_file(replica_hills_file);
replica_hills_os = cvm::proxy->output_stream(replica_hills_file);
if (!replica_hills_os) return cvm::get_error();
replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
return COLVARS_OK;
error_code |= proxy->remove_file(replica_hills_file);
std::ostream *replica_hills_os = proxy->output_stream(replica_hills_file);
if (replica_hills_os) {
replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
} else {
error_code |= FILE_ERROR;
}
return error_code;
}
@ -1883,5 +1895,3 @@ std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)
return os;
}

8
lib/colvars/colvarbias_meta.h
View File

@ -215,9 +215,12 @@ protected:
/// \brief Read new data from replicas' files
virtual void read_replica_files();
/// \brief Write data to other replicas
/// Write full state information to be read by other replicas
virtual int write_replica_state_file();
/// Call this after write_replica_state_file()
virtual int reopen_replica_buffer_file();
/// \brief Additional, "mirror" metadynamics biases, to collect info
/// from the other replicas
///
@ -251,9 +254,6 @@ protected:
/// This file becomes empty after replica_state_file is rewritten
std::string replica_hills_file;
/// \brief Output stream corresponding to replica_hills_file
std::ostream *replica_hills_os;
/// Position within replica_hills_file (when reading it)
int replica_hills_file_pos;

3
lib/colvars/colvarbias_restraint.cpp
View File

@ -1295,7 +1295,8 @@ colvarvalue const colvarbias_restraint_linear::restraint_force(size_t i) const
cvm::real colvarbias_restraint_linear::d_restraint_potential_dk(size_t i) const
{
return 1.0 / variables(i)->width * (variables(i)->value() - colvar_centers[i]);
return 1.0 / variables(i)->width * (variables(i)->value() -
colvar_centers[i]).sum();
}

2
lib/colvars/colvarcomp.cpp
View File

@ -7,6 +7,8 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <algorithm>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvar.h"

226
lib/colvars/colvarcomp.h
View File

@ -24,6 +24,13 @@
#include "colvar.h"
#include "colvaratoms.h"
#if (__cplusplus >= 201103L)
#include "colvar_geometricpath.h"
#include <functional>
#endif // C++11 checking
#include <map>
/// \brief Colvar component (base class for collective variables)
///
@ -688,9 +695,6 @@ protected:
/// Reference coordinates
std::vector<cvm::atom_pos> ref_pos;
/// Geometric center of the reference coordinates
cvm::atom_pos ref_pos_center;
/// Eigenvector (of a normal or essential mode): will always have zero center
std::vector<cvm::rvector> eigenvec;
@ -1383,6 +1387,222 @@ public:
};
class colvar::componentDisabled
: public colvar::cvc
{
public:
componentDisabled(std::string const &conf) {
cvm::error("Error: this component is not enabled in the current build; please see https://colvars.github.io/README-c++11.html");
}
virtual ~componentDisabled() {}
virtual void calc_value() {}
virtual void calc_gradients() {}
virtual void apply_force(colvarvalue const &force) {}
};
#if (__cplusplus >= 201103L)
class colvar::CartesianBasedPath
: public colvar::cvc
{
protected:
virtual void computeReferenceDistance(std::vector<cvm::real>& result);
/// Selected atoms
cvm::atom_group *atoms;
/// Fitting options
bool has_user_defined_fitting;
/// Reference frames
std::vector<std::vector<cvm::atom_pos>> reference_frames;
std::vector<std::vector<cvm::atom_pos>> reference_fitting_frames;
/// Atom groups for RMSD calculation together with reference frames
std::vector<cvm::atom_group*> comp_atoms;
/// Total number of reference frames
size_t total_reference_frames;
public:
CartesianBasedPath(std::string const &conf);
virtual ~CartesianBasedPath();
virtual void calc_value() = 0;
virtual void apply_force(colvarvalue const &force) = 0;
};
/// \brief Colvar component: alternative path collective variable using geometry, variable s
/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html
/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
class colvar::gspath
: public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S>
{
private:
// Optimal rotation for compute v3
cvm::rotation rot_v3;
protected:
virtual void prepareVectors();
virtual void updateReferenceDistances();
public:
gspath(std::string const &conf);
virtual ~gspath() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
};
/// \brief Colvar component: alternative path collective variable using geometry, variable z
/// This should be merged with gspath in the same class by class inheritance or something else
class colvar::gzpath
: public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::Z>
{
private:
// Optimal rotation for compute v3, v4
cvm::rotation rot_v3;
cvm::rotation rot_v4;
protected:
virtual void prepareVectors();
virtual void updateReferenceDistances();
public:
gzpath(std::string const &conf);
virtual ~gzpath() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
};
/// Current only linear combination of sub-CVCs is available
class colvar::linearCombination
: public colvar::cvc
{
protected:
/// Map from string to the types of colvar components
std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> string_cv_map;
/// Sub-colvar components
std::vector<colvar::cvc*> cv;
/// If all sub-cvs use explicit gradients then we also use it
bool use_explicit_gradients;
protected:
cvm::real getPolynomialFactorOfCVGradient(size_t i_cv) const;
public:
linearCombination(std::string const &conf);
virtual ~linearCombination();
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
};
class colvar::CVBasedPath
: public colvar::cvc
{
protected:
/// Map from string to the types of colvar components
std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> string_cv_map;
/// Sub-colvar components
std::vector<colvar::cvc*> cv;
/// Refernce colvar values from path
std::vector<std::vector<colvarvalue>> ref_cv;
/// If all sub-cvs use explicit gradients then we also use it
bool use_explicit_gradients;
/// Total number of reference frames
size_t total_reference_frames;
protected:
virtual void computeReferenceDistance(std::vector<cvm::real>& result);
cvm::real getPolynomialFactorOfCVGradient(size_t i_cv) const;
public:
CVBasedPath(std::string const &conf);
virtual ~CVBasedPath();
virtual void calc_value() = 0;
virtual void apply_force(colvarvalue const &force) = 0;
};
/// \brief Colvar component: alternative path collective variable using geometry, variable s
/// Allow any combination of existing (scalar) CVs
/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html
/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
class colvar::gspathCV
: public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>
{
protected:
virtual void updateReferenceDistances();
virtual void prepareVectors();
public:
gspathCV(std::string const &conf);
virtual ~gspathCV();
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
};
class colvar::gzpathCV
: public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::Z>
{
protected:
virtual void updateReferenceDistances();
virtual void prepareVectors();
public:
gzpathCV(std::string const &conf);
virtual ~gzpathCV();
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
};
#else // if the compiler doesn't support C++11
class colvar::linearCombination
: public colvar::componentDisabled
{
public:
linearCombination(std::string const &conf) : componentDisabled(conf) {}
};
class colvar::CartesianBasedPath
: public colvar::componentDisabled
{
public:
CartesianBasedPath(std::string const &conf) : componentDisabled(conf) {}
};
class colvar::CVBasedPath
: public colvar::componentDisabled
{
public:
CVBasedPath(std::string const &conf) : componentDisabled(conf) {}
};
class colvar::gspath
: public colvar::componentDisabled
{
public:
gspath(std::string const &conf) : componentDisabled(conf) {}
};
class colvar::gzpath
: public colvar::componentDisabled
{
public:
gzpath(std::string const &conf) : componentDisabled(conf) {}
};
class colvar::gspathCV
: public colvar::componentDisabled
{
public:
gspathCV(std::string const &conf) : componentDisabled(conf) {}
};
class colvar::gzpathCV
: public colvar::componentDisabled
{
public:
gzpathCV(std::string const &conf) : componentDisabled(conf) {}
};
#endif // C++11 checking
// metrics functions for cvc implementations
// simple definitions of the distance functions; these are useful only

8
lib/colvars/colvarcomp_distances.cpp
View File

@ -1013,8 +1013,7 @@ colvar::rmsd::rmsd(std::string const &conf)
cvm::to_str(atoms->size())+").\n");
return;
}
}
{
} else { // Only look for ref pos file if ref positions not already provided
std::string ref_pos_file;
if (get_keyval(conf, "refPositionsFile", ref_pos_file, std::string(""))) {
@ -1041,12 +1040,15 @@ colvar::rmsd::rmsd(std::string const &conf)
cvm::load_coords(ref_pos_file.c_str(), &ref_pos, atoms,
ref_pos_col, ref_pos_col_value);
} else {
cvm::error("Error: no reference positions for RMSD; use either refPositions of refPositionsFile.");
return;
}
}
if (ref_pos.size() != atoms->size()) {
cvm::error("Error: found " + cvm::to_str(ref_pos.size()) +
" reference positions; expected " + cvm::to_str(atoms->size()));
" reference positions for RMSD; expected " + cvm::to_str(atoms->size()));
return;
}

910
lib/colvars/colvarcomp_gpath.cpp Normal file
View File

@ -0,0 +1,910 @@
#if (__cplusplus >= 201103L)
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <numeric>
#include <algorithm>
#include <cmath>
#include <cstdlib>
#include <limits>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
#include "colvar.h"
#include "colvarcomp.h"
namespace GeometricPathCV {
void init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& conf)>>& string_cv_map);
}
bool compareColvarComponent(colvar::cvc *i, colvar::cvc *j)
{
return i->name < j->name;
}
colvar::CartesianBasedPath::CartesianBasedPath(std::string const &conf): cvc(conf), atoms(nullptr), reference_frames(0) {
// Parse selected atoms
atoms = parse_group(conf, "atoms");
has_user_defined_fitting = false;
std::string fitting_conf;
if (key_lookup(conf, "fittingAtoms", &fitting_conf)) {
has_user_defined_fitting = true;
}
// Lookup reference column of PDB
// Copied from the RMSD class
std::string reference_column;
double reference_column_value;
if (get_keyval(conf, "refPositionsCol", reference_column, std::string(""))) {
bool found = get_keyval(conf, "refPositionsColValue", reference_column_value, 0.0);
if (found && reference_column_value == 0.0) {
cvm::error("Error: refPositionsColValue, "
"if provided, must be non-zero.\n");
return;
}
}
// Lookup all reference frames
bool has_frames = true;
total_reference_frames = 0;
while (has_frames) {
std::string reference_position_file_lookup = "refPositionsFile" + cvm::to_str(total_reference_frames + 1);
if (key_lookup(conf, reference_position_file_lookup.c_str())) {
std::string reference_position_filename;
get_keyval(conf, reference_position_file_lookup.c_str(), reference_position_filename, std::string(""));
std::vector<cvm::atom_pos> reference_position(atoms->size());
cvm::load_coords(reference_position_filename.c_str(), &reference_position, atoms, reference_column, reference_column_value);
reference_frames.push_back(reference_position);
++total_reference_frames;
} else {
has_frames = false;
}
}
// Setup alignment to compute RMSD with respect to reference frames
for (size_t i_frame = 0; i_frame < reference_frames.size(); ++i_frame) {
cvm::atom_group* tmp_atoms = parse_group(conf, "atoms");
if (!has_user_defined_fitting) {
// Swipe from the rmsd class
tmp_atoms->b_center = true;
tmp_atoms->b_rotate = true;
tmp_atoms->ref_pos = reference_frames[i_frame];
tmp_atoms->center_ref_pos();
tmp_atoms->enable(f_ag_fit_gradients);
tmp_atoms->rot.request_group1_gradients(tmp_atoms->size());
tmp_atoms->rot.request_group2_gradients(tmp_atoms->size());
comp_atoms.push_back(tmp_atoms);
} else {
// parse a group of atoms for fitting
std::string fitting_group_name = std::string("fittingAtoms") + cvm::to_str(i_frame);
cvm::atom_group* tmp_fitting_atoms = new cvm::atom_group(fitting_group_name.c_str());
tmp_fitting_atoms->parse(fitting_conf);
tmp_fitting_atoms->disable(f_ag_scalable);
tmp_fitting_atoms->disable(f_ag_scalable_com);
tmp_fitting_atoms->fit_gradients.assign(tmp_fitting_atoms->size(), cvm::atom_pos(0.0, 0.0, 0.0));
std::string reference_position_file_lookup = "refPositionsFile" + cvm::to_str(i_frame + 1);
std::string reference_position_filename;
get_keyval(conf, reference_position_file_lookup.c_str(), reference_position_filename, std::string(""));
std::vector<cvm::atom_pos> reference_fitting_position(tmp_fitting_atoms->size());
cvm::load_coords(reference_position_filename.c_str(), &reference_fitting_position, tmp_fitting_atoms, reference_column, reference_column_value);
// setup the atom group for calculating
tmp_atoms->b_center = true;
tmp_atoms->b_rotate = true;
tmp_atoms->b_user_defined_fit = true;
tmp_atoms->disable(f_ag_scalable);
tmp_atoms->disable(f_ag_scalable_com);
tmp_atoms->ref_pos = reference_fitting_position;
tmp_atoms->center_ref_pos();
tmp_atoms->enable(f_ag_fit_gradients);
tmp_atoms->enable(f_ag_fitting_group);
tmp_atoms->fitting_group = tmp_fitting_atoms;
tmp_atoms->rot.request_group1_gradients(tmp_fitting_atoms->size());
tmp_atoms->rot.request_group2_gradients(tmp_fitting_atoms->size());
reference_fitting_frames.push_back(reference_fitting_position);
comp_atoms.push_back(tmp_atoms);
}
}
x.type(colvarvalue::type_scalar);
// Don't use implicit gradient
enable(f_cvc_explicit_gradient);
}
colvar::CartesianBasedPath::~CartesianBasedPath() {
for (auto it_comp_atoms = comp_atoms.begin(); it_comp_atoms != comp_atoms.end(); ++it_comp_atoms) {
if (*it_comp_atoms != nullptr) {
delete (*it_comp_atoms);
(*it_comp_atoms) = nullptr;
}
}
}
void colvar::CartesianBasedPath::computeReferenceDistance(std::vector<cvm::real>& result) {
for (size_t i_frame = 0; i_frame < reference_frames.size(); ++i_frame) {
cvm::real frame_rmsd = 0.0;
for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
frame_rmsd += ((*(comp_atoms[i_frame]))[i_atom].pos - reference_frames[i_frame][i_atom]).norm2();
}
frame_rmsd /= cvm::real(atoms->size());
frame_rmsd = cvm::sqrt(frame_rmsd);
result[i_frame] = frame_rmsd;
}
}
colvar::gspath::gspath(std::string const &conf): CartesianBasedPath(conf) {
function_type = "gspath";
get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
if (use_second_closest_frame == true) {
cvm::log(std::string("Geometric path s(σ) will use the second closest frame to compute s_(m-1)\n"));
} else {
cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m-1)\n"));
}
get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
if (use_third_closest_frame == true) {
cvm::log(std::string("Geometric path s(σ) will use the third closest frame to compute s_(m+1)\n"));
} else {
cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n"));
}
GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S>::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame);
cvm::log(std::string("Geometric pathCV(s) is initialized.\n"));
cvm::log(std::string("Geometric pathCV(s) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n"));
}
void colvar::gspath::updateReferenceDistances() {
computeReferenceDistance(frame_distances);
}
void colvar::gspath::prepareVectors() {
size_t i_atom;
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
// v1 = s_m - z
v1[i_atom] = reference_frames[min_frame_index_1][i_atom] - (*(comp_atoms[min_frame_index_1]))[i_atom].pos;
// v2 = z - s_(m-1)
v2[i_atom] = (*(comp_atoms[min_frame_index_2]))[i_atom].pos - reference_frames[min_frame_index_2][i_atom];
}
if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
cvm::atom_pos reference_cog_1, reference_cog_2;
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
reference_cog_1 += reference_frames[min_frame_index_1][i_atom];
reference_cog_2 += reference_frames[min_frame_index_2][i_atom];
}
reference_cog_1 /= reference_frames[min_frame_index_1].size();
reference_cog_2 /= reference_frames[min_frame_index_2].size();
std::vector<cvm::atom_pos> tmp_reference_frame_1(reference_frames[min_frame_index_1].size());
std::vector<cvm::atom_pos> tmp_reference_frame_2(reference_frames[min_frame_index_2].size());
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1;
tmp_reference_frame_2[i_atom] = reference_frames[min_frame_index_2][i_atom] - reference_cog_2;
}
if (has_user_defined_fitting) {
cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2;
for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom];
reference_fitting_cog_2 += reference_fitting_frames[min_frame_index_2][i_atom];
}
reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size();
reference_fitting_cog_2 /= reference_fitting_frames[min_frame_index_2].size();
std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1(reference_fitting_frames[min_frame_index_1].size());
std::vector<cvm::atom_pos> tmp_reference_fitting_frame_2(reference_fitting_frames[min_frame_index_2].size());
for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1;
tmp_reference_fitting_frame_2[i_atom] = reference_fitting_frames[min_frame_index_2][i_atom] - reference_fitting_cog_2;
}
rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_2);
} else {
rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2);
}
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
v3[i_atom] = rot_v3.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom];
}
} else {
cvm::atom_pos reference_cog_1, reference_cog_3;
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
reference_cog_1 += reference_frames[min_frame_index_1][i_atom];
reference_cog_3 += reference_frames[min_frame_index_3][i_atom];
}
reference_cog_1 /= reference_frames[min_frame_index_1].size();
reference_cog_3 /= reference_frames[min_frame_index_3].size();
std::vector<cvm::atom_pos> tmp_reference_frame_1(reference_frames[min_frame_index_1].size());
std::vector<cvm::atom_pos> tmp_reference_frame_3(reference_frames[min_frame_index_3].size());
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1;
tmp_reference_frame_3[i_atom] = reference_frames[min_frame_index_3][i_atom] - reference_cog_3;
}
if (has_user_defined_fitting) {
cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_3;
for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom];
reference_fitting_cog_3 += reference_fitting_frames[min_frame_index_3][i_atom];
}
reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size();
reference_fitting_cog_3 /= reference_fitting_frames[min_frame_index_3].size();
std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1(reference_fitting_frames[min_frame_index_1].size());
std::vector<cvm::atom_pos> tmp_reference_fitting_frame_3(reference_fitting_frames[min_frame_index_3].size());
for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1;
tmp_reference_fitting_frame_3[i_atom] = reference_fitting_frames[min_frame_index_3][i_atom] - reference_fitting_cog_3;
}
rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_3);
} else {
rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3);
}
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
// v3 = s_(m+1) - s_m
v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]);
}
}
}
void colvar::gspath::calc_value() {
computeValue();
x = s;
}
void colvar::gspath::calc_gradients() {
computeDerivatives();
cvm::rvector tmp_atom_grad_v1, tmp_atom_grad_v2;
// dS(v1, v2(r), v3) / dr = ∂S/∂v1 * dv1/dr + ∂S/∂v2 * dv2/dr
// dv1/dr = [fitting matrix 1][-1, ..., -1]
// dv2/dr = [fitting matrix 2][1, ..., 1]
// ∂S/∂v1 = ± (∂f/∂v1) / (2M)
// ∂S/∂v2 = ± (∂f/∂v2) / (2M)
// dS(v1, v2(r), v3) / dr = -1.0 * ± (∂f/∂v1) / (2M) + ± (∂f/∂v2) / (2M)
for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
tmp_atom_grad_v1[0] = -1.0 * sign * 0.5 * dfdv1[i_atom][0] / M;
tmp_atom_grad_v1[1] = -1.0 * sign * 0.5 * dfdv1[i_atom][1] / M;
tmp_atom_grad_v1[2] = -1.0 * sign * 0.5 * dfdv1[i_atom][2] / M;
tmp_atom_grad_v2[0] = sign * 0.5 * dfdv2[i_atom][0] / M;
tmp_atom_grad_v2[1] = sign * 0.5 * dfdv2[i_atom][1] / M;
tmp_atom_grad_v2[2] = sign * 0.5 * dfdv2[i_atom][2] / M;
(*(comp_atoms[min_frame_index_1]))[i_atom].grad += tmp_atom_grad_v1;
(*(comp_atoms[min_frame_index_2]))[i_atom].grad += tmp_atom_grad_v2;
}
}
void colvar::gspath::apply_force(colvarvalue const &force) {
// The force applied to this CV is scalar type
cvm::real const &F = force.real_value;
(*(comp_atoms[min_frame_index_1])).apply_colvar_force(F);
(*(comp_atoms[min_frame_index_2])).apply_colvar_force(F);
}
colvar::gzpath::gzpath(std::string const &conf): CartesianBasedPath(conf) {
function_type = "gzpath";
get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
if (use_second_closest_frame == true) {
cvm::log(std::string("Geometric path z(σ) will use the second closest frame to compute s_(m-1)\n"));
} else {
cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m-1)\n"));
}
get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
if (use_third_closest_frame == true) {
cvm::log(std::string("Geometric path z(σ) will use the third closest frame to compute s_(m+1)\n"));
} else {
cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m+1)\n"));
}
bool b_use_z_square = false;
get_keyval(conf, "useZsquare", b_use_z_square, false);
if (b_use_z_square == true) {
cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n"));
}
GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::Z>::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square);
// Logging
cvm::log(std::string("Geometric pathCV(z) is initialized.\n"));
cvm::log(std::string("Geometric pathCV(z) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n"));
}
void colvar::gzpath::updateReferenceDistances() {
computeReferenceDistance(frame_distances);
}
void colvar::gzpath::prepareVectors() {
cvm::atom_pos reference_cog_1, reference_cog_2;
size_t i_atom;
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
reference_cog_1 += reference_frames[min_frame_index_1][i_atom];
reference_cog_2 += reference_frames[min_frame_index_2][i_atom];
}
reference_cog_1 /= reference_frames[min_frame_index_1].size();
reference_cog_2 /= reference_frames[min_frame_index_2].size();
std::vector<cvm::atom_pos> tmp_reference_frame_1(reference_frames[min_frame_index_1].size());
std::vector<cvm::atom_pos> tmp_reference_frame_2(reference_frames[min_frame_index_2].size());
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1;
tmp_reference_frame_2[i_atom] = reference_frames[min_frame_index_2][i_atom] - reference_cog_2;
}
std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1;
std::vector<cvm::atom_pos> tmp_reference_fitting_frame_2;
if (has_user_defined_fitting) {
cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2;
for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom];
reference_fitting_cog_2 += reference_fitting_frames[min_frame_index_2][i_atom];
}
reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size();
reference_fitting_cog_2 /= reference_fitting_frames[min_frame_index_2].size();
tmp_reference_fitting_frame_1.resize(reference_fitting_frames[min_frame_index_1].size());
tmp_reference_fitting_frame_2.resize(reference_fitting_frames[min_frame_index_2].size());
for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1;
tmp_reference_fitting_frame_2[i_atom] = reference_fitting_frames[min_frame_index_2][i_atom] - reference_fitting_cog_2;
}
rot_v4.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_2);
} else {
rot_v4.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2);
}
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
v1[i_atom] = reference_frames[min_frame_index_1][i_atom] - (*(comp_atoms[min_frame_index_1]))[i_atom].pos;
v2[i_atom] = (*(comp_atoms[min_frame_index_2]))[i_atom].pos - reference_frames[min_frame_index_2][i_atom];
// v4 only computes in gzpath
// v4 = s_m - s_(m-1)
v4[i_atom] = rot_v4.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom];
}
if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
v3 = v4;
} else {
cvm::atom_pos reference_cog_3;
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
reference_cog_3 += reference_frames[min_frame_index_3][i_atom];
}
reference_cog_3 /= reference_frames[min_frame_index_3].size();
std::vector<cvm::atom_pos> tmp_reference_frame_3(reference_frames[min_frame_index_3].size());
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
tmp_reference_frame_3[i_atom] = reference_frames[min_frame_index_3][i_atom] - reference_cog_3;
}
if (has_user_defined_fitting) {
cvm::atom_pos reference_fitting_cog_3;
for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_3].size(); ++i_atom) {
reference_fitting_cog_3 += reference_fitting_frames[min_frame_index_3][i_atom];
}
reference_fitting_cog_3 /= reference_fitting_frames[min_frame_index_3].size();
std::vector<cvm::atom_pos> tmp_reference_fitting_frame_3(reference_fitting_frames[min_frame_index_3].size());
for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_3].size(); ++i_atom) {
tmp_reference_fitting_frame_3[i_atom] = reference_fitting_frames[min_frame_index_3][i_atom] - reference_fitting_cog_3;
}
rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_3);
} else {
rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3);
}
for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
// v3 = s_(m+1) - s_m
v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]);
}
}
}
void colvar::gzpath::calc_value() {
computeValue();
x = z;
}
void colvar::gzpath::calc_gradients() {
computeDerivatives();
cvm::rvector tmp_atom_grad_v1, tmp_atom_grad_v2;
for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
tmp_atom_grad_v1 = -1.0 * dzdv1[i_atom];
tmp_atom_grad_v2 = dzdv2[i_atom];
(*(comp_atoms[min_frame_index_1]))[i_atom].grad += tmp_atom_grad_v1;
(*(comp_atoms[min_frame_index_2]))[i_atom].grad += tmp_atom_grad_v2;
}
}
void colvar::gzpath::apply_force(colvarvalue const &force) {
// The force applied to this CV is scalar type
cvm::real const &F = force.real_value;
(*(comp_atoms[min_frame_index_1])).apply_colvar_force(F);
(*(comp_atoms[min_frame_index_2])).apply_colvar_force(F);
}
colvar::linearCombination::linearCombination(std::string const &conf): cvc(conf) {
GeometricPathCV::init_string_cv_map(string_cv_map);
// Lookup all available sub-cvcs
for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
if (key_lookup(conf, it_cv_map->first.c_str())) {
std::vector<std::string> sub_cvc_confs;
get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
for (auto it_sub_cvc_conf = sub_cvc_confs.begin(); it_sub_cvc_conf != sub_cvc_confs.end(); ++it_sub_cvc_conf) {
cv.push_back((it_cv_map->second)(*(it_sub_cvc_conf)));
}
}
}
// Sort all sub CVs by their names
std::sort(cv.begin(), cv.end(), compareColvarComponent);
for (auto it_sub_cv = cv.begin(); it_sub_cv != cv.end(); ++it_sub_cv) {
for (auto it_atom_group = (*it_sub_cv)->atom_groups.begin(); it_atom_group != (*it_sub_cv)->atom_groups.end(); ++it_atom_group) {
register_atom_group(*it_atom_group);
}
}
x.type(cv[0]->value());
x.reset();
use_explicit_gradients = true;
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
use_explicit_gradients = false;
}
}
if (!use_explicit_gradients) {
disable(f_cvc_explicit_gradient);
}
}
cvm::real colvar::linearCombination::getPolynomialFactorOfCVGradient(size_t i_cv) const {
cvm::real factor_polynomial = 1.0;
if (cv[i_cv]->value().type() == colvarvalue::type_scalar) {
factor_polynomial = cv[i_cv]->sup_coeff * cv[i_cv]->sup_np * cvm::pow(cv[i_cv]->value().real_value, cv[i_cv]->sup_np - 1);
} else {
factor_polynomial = cv[i_cv]->sup_coeff;
}
return factor_polynomial;
}
colvar::linearCombination::~linearCombination() {
for (auto it = cv.begin(); it != cv.end(); ++it) {
delete (*it);
}
}
void colvar::linearCombination::calc_value() {
x.reset();
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
cv[i_cv]->calc_value();
colvarvalue current_cv_value(cv[i_cv]->value());
// polynomial combination allowed
if (current_cv_value.type() == colvarvalue::type_scalar) {
x += cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np));
} else {
x += cv[i_cv]->sup_coeff * current_cv_value;
}
}
}
void colvar::linearCombination::calc_gradients() {
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
cv[i_cv]->calc_gradients();
if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
!cv[i_cv]->is_enabled(f_cvc_scalable) &&
!cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
(*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad;
}
}
}
}
}
}
void colvar::linearCombination::apply_force(colvarvalue const &force) {
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
// If this CV us explicit gradients, then atomic gradients is already calculated
// We can apply the force to atom groups directly
if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
!cv[i_cv]->is_enabled(f_cvc_scalable) &&
!cv[i_cv]->is_enabled(f_cvc_scalable_com)
) {
for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
(cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
}
} else {
// Compute factors for polynomial combinations
cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
colvarvalue cv_force = force.real_value * factor_polynomial;
cv[i_cv]->apply_force(cv_force);
}
}
}
colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
GeometricPathCV::init_string_cv_map(string_cv_map);
// Lookup all available sub-cvcs
for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
if (key_lookup(conf, it_cv_map->first.c_str())) {
std::vector<std::string> sub_cvc_confs;
get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
for (auto it_sub_cvc_conf = sub_cvc_confs.begin(); it_sub_cvc_conf != sub_cvc_confs.end(); ++it_sub_cvc_conf) {
cv.push_back((it_cv_map->second)(*(it_sub_cvc_conf)));
}
}
}
// Sort all sub CVs by their names
std::sort(cv.begin(), cv.end(), compareColvarComponent);
// Register atom groups and determine the colvar type for reference
std::vector<colvarvalue> tmp_cv;
for (auto it_sub_cv = cv.begin(); it_sub_cv != cv.end(); ++it_sub_cv) {
for (auto it_atom_group = (*it_sub_cv)->atom_groups.begin(); it_atom_group != (*it_sub_cv)->atom_groups.end(); ++it_atom_group) {
register_atom_group(*it_atom_group);
}
colvarvalue tmp_i_cv((*it_sub_cv)->value());
tmp_i_cv.reset();
tmp_cv.push_back(tmp_i_cv);
}
// Read path file
// Lookup all reference CV values
std::string path_filename;
get_keyval(conf, "pathFile", path_filename);
cvm::log(std::string("Reading path file: ") + path_filename + std::string("\n"));
std::ifstream ifs_path(path_filename);
if (!ifs_path.is_open()) {
cvm::error("Error: failed to open path file.\n");
}
std::string line;
const std::string token(" ");
total_reference_frames = 0;
while (std::getline(ifs_path, line)) {
std::vector<std::string> fields;
split_string(line, token, fields);
size_t num_value_required = 0;
for (size_t i_cv = 0; i_cv < tmp_cv.size(); ++i_cv) {
const size_t value_size = tmp_cv[i_cv].size();
num_value_required += value_size;
cvm::log(std::string("Reading CV ") + cv[i_cv]->name + std::string(" with ") + cvm::to_str(value_size) + std::string(" value(s)\n"));
if (num_value_required <= fields.size()) {
size_t start_index = num_value_required - value_size;
for (size_t i = start_index; i < num_value_required; ++i) {
tmp_cv[i_cv][i] = std::atof(fields[i].c_str());
cvm::log(fields[i] + std::string(" "));
}
cvm::log(std::string("\n"));
} else {
cvm::error("Error: incorrect format of path file.\n");
}
}
if (!fields.empty()) {
ref_cv.push_back(tmp_cv);
++total_reference_frames;
}
}
x.type(colvarvalue::type_scalar);
use_explicit_gradients = true;
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
use_explicit_gradients = false;
}
}
if (!use_explicit_gradients) {
disable(f_cvc_explicit_gradient);
}
}
void colvar::CVBasedPath::computeReferenceDistance(std::vector<cvm::real>& result) {
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
cv[i_cv]->calc_value();
}
for (size_t i_frame = 0; i_frame < ref_cv.size(); ++i_frame) {
cvm::real rmsd_i = 0.0;
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
colvarvalue ref_cv_value(ref_cv[i_frame][i_cv]);
colvarvalue current_cv_value(cv[i_cv]->value());
// polynomial combination allowed
if (current_cv_value.type() == colvarvalue::type_scalar) {
// wrapping is already in dist2
rmsd_i += cv[i_cv]->dist2(cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)), ref_cv_value.real_value);
} else {
rmsd_i += cv[i_cv]->dist2(cv[i_cv]->sup_coeff * current_cv_value, ref_cv_value);
}
}
rmsd_i /= cvm::real(cv.size());
rmsd_i = cvm::sqrt(rmsd_i);
result[i_frame] = rmsd_i;
}
}
cvm::real colvar::CVBasedPath::getPolynomialFactorOfCVGradient(size_t i_cv) const {
cvm::real factor_polynomial = 1.0;
if (cv[i_cv]->value().type() == colvarvalue::type_scalar) {
factor_polynomial = cv[i_cv]->sup_coeff * cv[i_cv]->sup_np * cvm::pow(cv[i_cv]->value().real_value, cv[i_cv]->sup_np - 1);
} else {
factor_polynomial = cv[i_cv]->sup_coeff;
}
return factor_polynomial;
}
colvar::CVBasedPath::~CVBasedPath() {
for (auto it = cv.begin(); it != cv.end(); ++it) {
delete (*it);
}
}
colvar::gspathCV::gspathCV(std::string const &conf): CVBasedPath(conf) {
function_type = "gspathCV";
cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
// Initialize variables for future calculation
get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
if (use_second_closest_frame == true) {
cvm::log(std::string("Geometric path s(σ) will use the second closest frame to compute s_(m-1)\n"));
} else {
cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m-1)\n"));
}
get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
if (use_third_closest_frame == true) {
cvm::log(std::string("Geometric path s(σ) will use the third closest frame to compute s_(m+1)\n"));
} else {
cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n"));
}
GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame);
x.type(colvarvalue::type_scalar);
use_explicit_gradients = true;
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
use_explicit_gradients = false;
}
}
if (!use_explicit_gradients) {
cvm::log("Geometric path s(σ) will use implicit gradients.\n");
disable(f_cvc_explicit_gradient);
}
}
colvar::gspathCV::~gspathCV() {}
void colvar::gspathCV::updateReferenceDistances() {
computeReferenceDistance(frame_distances);
}
void colvar::gspathCV::prepareVectors() {
// Compute v1, v2 and v3
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
// values of sub-cvc are computed in update_distances
// cv[i_cv]->calc_value();
colvarvalue f1_ref_cv_i_value(ref_cv[min_frame_index_1][i_cv]);
colvarvalue f2_ref_cv_i_value(ref_cv[min_frame_index_2][i_cv]);
colvarvalue current_cv_value(cv[i_cv]->value());
// polynomial combination allowed
if (current_cv_value.type() == colvarvalue::type_scalar) {
v1[i_cv] = f1_ref_cv_i_value.real_value - cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np));
v2[i_cv] = cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)) - f2_ref_cv_i_value.real_value;
} else {
v1[i_cv] = f1_ref_cv_i_value - cv[i_cv]->sup_coeff * current_cv_value;
v2[i_cv] = cv[i_cv]->sup_coeff * current_cv_value - f2_ref_cv_i_value;
}
cv[i_cv]->wrap(v1[i_cv]);
cv[i_cv]->wrap(v2[i_cv]);
}
if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
v3[i_cv] = ref_cv[min_frame_index_1][i_cv] - ref_cv[min_frame_index_2][i_cv];
cv[i_cv]->wrap(v3[i_cv]);
}
} else {
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
v3[i_cv] = ref_cv[min_frame_index_3][i_cv] - ref_cv[min_frame_index_1][i_cv];
cv[i_cv]->wrap(v3[i_cv]);
}
}
}
void colvar::gspathCV::calc_value() {
computeValue();
x = s;
}
void colvar::gspathCV::calc_gradients() {
computeDerivatives();
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
// No matter whether the i-th cv uses implicit gradient, compute it first.
cv[i_cv]->calc_gradients();
// If the gradient is not implicit, then add the gradients to its atom groups
if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
!cv[i_cv]->is_enabled(f_cvc_scalable) &&
!cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
// Temporary variables storing gradients
colvarvalue tmp_cv_grad_v1(cv[i_cv]->value());
colvarvalue tmp_cv_grad_v2(cv[i_cv]->value());
// Compute factors for polynomial combinations
cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
// Loop over all elements of the corresponding colvar value
for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
// ds/dz, z = vector of CVs
tmp_cv_grad_v1[j_elem] = -1.0 * sign * 0.5 * dfdv1[i_cv][j_elem] / M;
tmp_cv_grad_v2[j_elem] = sign * 0.5 * dfdv2[i_cv][j_elem] / M;
// Apply the gradients to the atom groups in i-th cv
// Loop over all atom groups
for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
// Loop over all atoms in the k-th atom group
for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
// Chain rule
(*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * ((*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v1[j_elem] + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v2[j_elem]);
}
}
}
}
}
}
void colvar::gspathCV::apply_force(colvarvalue const &force) {
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
// If this CV us explicit gradients, then atomic gradients is already calculated
// We can apply the force to atom groups directly
if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
!cv[i_cv]->is_enabled(f_cvc_scalable) &&
!cv[i_cv]->is_enabled(f_cvc_scalable_com)
) {
for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
(cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
}
} else {
// Temporary variables storing gradients
colvarvalue tmp_cv_grad_v1(cv[i_cv]->value());
colvarvalue tmp_cv_grad_v2(cv[i_cv]->value());
// Compute factors for polynomial combinations
cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
// ds/dz, z = vector of CVs
tmp_cv_grad_v1[j_elem] = -1.0 * sign * 0.5 * dfdv1[i_cv][j_elem] / M;
tmp_cv_grad_v2[j_elem] = sign * 0.5 * dfdv2[i_cv][j_elem] / M;
}
colvarvalue cv_force = force.real_value * factor_polynomial * (tmp_cv_grad_v1 + tmp_cv_grad_v2);
cv[i_cv]->apply_force(cv_force);
}
}
}
colvar::gzpathCV::gzpathCV(std::string const &conf): CVBasedPath(conf) {
function_type = "gzpathCV";
cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
// Initialize variables for future calculation
M = cvm::real(total_reference_frames - 1);
m = 1.0;
get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
if (use_second_closest_frame == true) {
cvm::log(std::string("Geometric path z(σ) will use the second closest frame to compute s_(m-1)\n"));
} else {
cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m-1)\n"));
}
get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
if (use_third_closest_frame == true) {
cvm::log(std::string("Geometric path z(σ) will use the third closest frame to compute s_(m+1)\n"));
} else {
cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m+1)\n"));
}
bool b_use_z_square = false;
get_keyval(conf, "useZsquare", b_use_z_square, false);
if (b_use_z_square == true) {
cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n"));
}
GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::Z>::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square);
x.type(colvarvalue::type_scalar);
use_explicit_gradients = true;
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
use_explicit_gradients = false;
}
}
if (!use_explicit_gradients) {
cvm::log("Geometric path z(σ) will use implicit gradients.\n");
disable(f_cvc_explicit_gradient);
}
}
colvar::gzpathCV::~gzpathCV() {
}
void colvar::gzpathCV::updateReferenceDistances() {
computeReferenceDistance(frame_distances);
}
void colvar::gzpathCV::prepareVectors() {
// Compute v1, v2 and v3
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
// values of sub-cvc are computed in update_distances
// cv[i_cv]->calc_value();
colvarvalue f1_ref_cv_i_value(ref_cv[min_frame_index_1][i_cv]);
colvarvalue f2_ref_cv_i_value(ref_cv[min_frame_index_2][i_cv]);
colvarvalue current_cv_value(cv[i_cv]->value());
// polynomial combination allowed
if (current_cv_value.type() == colvarvalue::type_scalar) {
v1[i_cv] = f1_ref_cv_i_value.real_value - cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np));
v2[i_cv] = cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)) - f2_ref_cv_i_value.real_value;
} else {
v1[i_cv] = f1_ref_cv_i_value - cv[i_cv]->sup_coeff * current_cv_value;
v2[i_cv] = cv[i_cv]->sup_coeff * current_cv_value - f2_ref_cv_i_value;
}
v4[i_cv] = f1_ref_cv_i_value - f2_ref_cv_i_value;
cv[i_cv]->wrap(v1[i_cv]);
cv[i_cv]->wrap(v2[i_cv]);
cv[i_cv]->wrap(v4[i_cv]);
}
if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
v3[i_cv] = ref_cv[min_frame_index_1][i_cv] - ref_cv[min_frame_index_2][i_cv];
cv[i_cv]->wrap(v3[i_cv]);
}
} else {
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
v3[i_cv] = ref_cv[min_frame_index_3][i_cv] - ref_cv[min_frame_index_1][i_cv];
cv[i_cv]->wrap(v3[i_cv]);
}
}
}
void colvar::gzpathCV::calc_value() {
computeValue();
x = z;
}
void colvar::gzpathCV::calc_gradients() {
computeDerivatives();
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
// No matter whether the i-th cv uses implicit gradient, compute it first.
cv[i_cv]->calc_gradients();
// If the gradient is not implicit, then add the gradients to its atom groups
if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
!cv[i_cv]->is_enabled(f_cvc_scalable) &&
!cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
// Temporary variables storing gradients
colvarvalue tmp_cv_grad_v1 = -1.0 * dzdv1[i_cv];
colvarvalue tmp_cv_grad_v2 = 1.0 * dzdv2[i_cv];
// Compute factors for polynomial combinations
cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
// Apply the gradients to the atom groups in i-th cv
// Loop over all atom groups
for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
// Loop over all atoms in the k-th atom group
for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
// Chain rule
(*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * ((*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v1[j_elem] + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v2[j_elem]);
}
}
}
}
}
}
void colvar::gzpathCV::apply_force(colvarvalue const &force) {
for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
// If this CV us explicit gradients, then atomic gradients is already calculated
// We can apply the force to atom groups directly
if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
!cv[i_cv]->is_enabled(f_cvc_scalable) &&
!cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
(cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
}
}
else {
colvarvalue tmp_cv_grad_v1 = -1.0 * dzdv1[i_cv];
colvarvalue tmp_cv_grad_v2 = 1.0 * dzdv2[i_cv];
// Temporary variables storing gradients
// Compute factors for polynomial combinations
cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
colvarvalue cv_force = force.real_value * factor_polynomial * (tmp_cv_grad_v1 + tmp_cv_grad_v2);
cv[i_cv]->apply_force(cv_force);
}
}
}
void GeometricPathCV::init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>& string_cv_map) {
string_cv_map["distance"] = [](const std::string& conf){return new colvar::distance(conf);};
string_cv_map["dihedral"] = [](const std::string& conf){return new colvar::dihedral(conf);};
string_cv_map["angle"] = [](const std::string& conf){return new colvar::angle(conf);};
string_cv_map["rmsd"] = [](const std::string& conf){return new colvar::rmsd(conf);};
string_cv_map["gyration"] = [](const std::string& conf){return new colvar::gyration(conf);};
string_cv_map["inertia"] = [](const std::string& conf){return new colvar::inertia(conf);};
string_cv_map["inertiaZ"] = [](const std::string& conf){return new colvar::inertia_z(conf);};
string_cv_map["tilt"] = [](const std::string& conf){return new colvar::tilt(conf);};
string_cv_map["distanceZ"] = [](const std::string& conf){return new colvar::distance_z(conf);};
string_cv_map["distanceXY"] = [](const std::string& conf){return new colvar::distance_xy(conf);};
string_cv_map["polarTheta"] = [](const std::string& conf){return new colvar::polar_theta(conf);};
string_cv_map["polarPhi"] = [](const std::string& conf){return new colvar::polar_phi(conf);};
string_cv_map["distanceVec"] = [](const std::string& conf){return new colvar::distance_vec(conf);};
string_cv_map["orientationAngle"] = [](const std::string& conf){return new colvar::orientation_angle(conf);};
string_cv_map["distancePairs"] = [](const std::string& conf){return new colvar::distance_pairs(conf);};
string_cv_map["dipoleMagnitude"] = [](const std::string& conf){return new colvar::dipole_magnitude(conf);};
string_cv_map["coordNum"] = [](const std::string& conf){return new colvar::coordnum(conf);};
string_cv_map["selfCoordNum"] = [](const std::string& conf){return new colvar::selfcoordnum(conf);};
string_cv_map["dipoleAngle"] = [](const std::string& conf){return new colvar::dipole_angle(conf);};
string_cv_map["orientation"] = [](const std::string& conf){return new colvar::orientation(conf);};
string_cv_map["orientationProj"] = [](const std::string& conf){return new colvar::orientation_proj(conf);};
string_cv_map["eigenvector"] = [](const std::string& conf){return new colvar::eigenvector(conf);};
string_cv_map["cartesian"] = [](const std::string& conf){return new colvar::cartesian(conf);};
string_cv_map["alpha"] = [](const std::string& conf){return new colvar::alpha_angles(conf);};
string_cv_map["dihedralPC"] = [](const std::string& conf){return new colvar::dihedPC(conf);};
string_cv_map["linearCombination"] = [](const std::string& conf){return new colvar::linearCombination(conf);};
}
#endif

2
lib/colvars/colvarcomp_protein.cpp
View File

@ -7,6 +7,8 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <algorithm>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"

4
lib/colvars/colvargrid.cpp
View File

@ -109,7 +109,9 @@ cvm::real colvar_grid_scalar::entropy() const
{
cvm::real sum = 0.0;
for (size_t i = 0; i < nt; i++) {
sum += -1.0 * data[i] * cvm::logn(data[i]);
if (data[i] >0) {
sum += -1.0 * data[i] * cvm::logn(data[i]);
}
}
cvm::real bin_volume = 1.0;
for (size_t id = 0; id < widths.size(); id++) {

6
lib/colvars/colvargrid.h
View File

@ -557,11 +557,11 @@ public:
data[i] *= a;
}
/// \brief Assign all zero elements a scalar constant (fast loop)
inline void remove_zeros(cvm::real const &a)
/// \brief Assign values that are smaller than scalar constant the latter value (fast loop)
inline void remove_small_values(cvm::real const &a)
{
for (size_t i = 0; i < nt; i++)
if(data[i]==0) data[i] = a;
if(data[i]<a) data[i] = a;
}

38
lib/colvars/colvarparse.cpp
View File

@ -7,7 +7,6 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <sstream>
#include <iostream>
#include <algorithm>
@ -58,6 +57,28 @@ bool colvarparse::get_key_string_value(std::string const &conf,
return b_found_any;
}
bool colvarparse::get_key_string_multi_value(std::string const &conf,
char const *key, std::vector<std::string>& data)
{
bool b_found = false, b_found_any = false;
size_t save_pos = 0, found_count = 0;
data.clear();
do {
std::string data_this = "";
b_found = key_lookup(conf, key, &data_this, &save_pos);
if (b_found) {
if (!b_found_any)
b_found_any = true;
found_count++;
data.push_back(data_this);
}
} while (b_found);
return b_found_any;
}
template<typename TYPE>
void colvarparse::mark_key_set_user(std::string const &key_str,
@ -843,3 +864,18 @@ int colvarparse::check_braces(std::string const &conf,
}
return (brace_count != 0) ? INPUT_ERROR : COLVARS_OK;
}
void colvarparse::split_string(const std::string& data, const std::string& delim, std::vector<std::string>& dest) {
size_t index = 0, new_index = 0;
std::string tmpstr;
while (index != data.length()) {
new_index = data.find(delim, index);
if (new_index != std::string::npos) tmpstr = data.substr(index, new_index - index);
else tmpstr = data.substr(index, data.length());
if (!tmpstr.empty()) {
dest.push_back(tmpstr);
}
if (new_index == std::string::npos) break;
index = new_index + 1;
}
}

10
lib/colvars/colvarparse.h
View File

@ -212,6 +212,10 @@ protected:
bool get_key_string_value(std::string const &conf,
char const *key, std::string &data);
/// Get multiple strings from repeated instances of a same keyword
bool get_key_string_multi_value(std::string const &conf,
char const *key, std::vector<std::string>& data);
/// Template for single-value keyword parsers
template<typename TYPE>
bool _get_keyval_scalar_(std::string const &conf,
@ -322,6 +326,12 @@ public:
/// from this position
static int check_braces(std::string const &conf, size_t const start_pos);
/// \brief Split a string with a specified delimiter into a vector
/// \param data The string to be splitted
/// \param delim A delimiter
/// \param dest A destination vector to store the splitted results
static void split_string(const std::string& data, const std::string& delim, std::vector<std::string>& dest);
protected:
/// \brief List of legal keywords for this object: this is updated

77
lib/colvars/colvarproxy.cpp
View File

@ -7,8 +7,14 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#if !defined(WIN32) || defined(__CYGWIN__)
#include <unistd.h>
#endif
#include <cerrno>
#include <sstream>
#include <cstring>
#include <cstdio>
#if defined(_OPENMP)
#include <omp.h>
@ -704,6 +710,27 @@ std::ostream * colvarproxy_io::output_stream(std::string const &output_name,
if (cvm::debug()) {
cvm::log("Using colvarproxy::output_stream()\n");
}
std::ostream *os = get_output_stream(output_name);
if (os != NULL) return os;
if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
backup_file(output_name);
}
std::ofstream *osf = new std::ofstream(output_name.c_str(), mode);
if (!osf->is_open()) {
cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
FILE_ERROR);
return NULL;
}
output_stream_names.push_back(output_name);
output_files.push_back(osf);
return osf;
}
std::ostream *colvarproxy_io::get_output_stream(std::string const &output_name)
{
std::list<std::ostream *>::iterator osi = output_files.begin();
std::list<std::string>::iterator osni = output_stream_names.begin();
for ( ; osi != output_files.end(); osi++, osni++) {
@ -711,21 +738,11 @@ std::ostream * colvarproxy_io::output_stream(std::string const &output_name,
return *osi;
}
}
if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
backup_file(output_name);
}
std::ofstream *os = new std::ofstream(output_name.c_str(), mode);
if (!os->is_open()) {
cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
FILE_ERROR);
return NULL;
}
output_stream_names.push_back(output_name);
output_files.push_back(os);
return os;
return NULL;
}
int colvarproxy_io::flush_output_stream(std::ostream *os)
{
std::list<std::ostream *>::iterator osi = output_files.begin();
@ -761,10 +778,45 @@ int colvarproxy_io::close_output_stream(std::string const &output_name)
int colvarproxy_io::backup_file(char const *filename)
{
// TODO implement this using rename_file()
return COLVARS_NOT_IMPLEMENTED;
}
int colvarproxy_io::remove_file(char const *filename)
{
if (std::remove(filename)) {
if (errno != ENOENT) {
return cvm::error("Error: in removing file \""+std::string(filename)+
"\".\n.",
FILE_ERROR);
}
}
return COLVARS_OK;
}
int colvarproxy_io::rename_file(char const *filename, char const *newfilename)
{
int error_code = COLVARS_OK;
#if defined(WIN32) && !defined(__CYGWIN__)
// On straight Windows, must remove the destination before renaming it
error_code |= remove_file(newfilename);
#endif
int rename_exit_code = 0;
while ((rename_exit_code = std::rename(filename, newfilename)) != 0) {
if (errno == EINTR) continue;
// Call log() instead of error to allow the next try
cvm::log("Error: in renaming file \""+std::string(filename)+"\" to \""+
std::string(newfilename)+"\".\n.");
error_code |= FILE_ERROR;
if (errno == EXDEV) continue;
break;
}
return rename_exit_code ? error_code : COLVARS_OK;
}
colvarproxy::colvarproxy()
{
@ -826,4 +878,3 @@ int colvarproxy::get_version_from_string(char const *version_string)
is >> newint;
return newint;
}

24
lib/colvars/colvarproxy.h
View File

@ -571,7 +571,10 @@ public:
/// if this is not open already, then open it
virtual std::ostream *output_stream(std::string const &output_name,
std::ios_base::openmode mode =
std::ios_base::out);
std::ios_base::out);
/// Returns a reference to output_name if it exists, NULL otherwise
virtual std::ostream *get_output_stream(std::string const &output_name);
/// \brief Flushes the given output channel
virtual int flush_output_stream(std::ostream *os);
@ -588,6 +591,25 @@ public:
return backup_file(filename.c_str());
}
/// Remove the given file
int remove_file(char const *filename);
/// Remove the given file
inline int remove_file(std::string const &filename)
{
return remove_file(filename.c_str());
}
/// Rename the given file
int rename_file(char const *filename, char const *newfilename);
/// Rename the given file
inline int rename_file(std::string const &filename,
std::string const &newfilename)
{
return rename_file(filename.c_str(), newfilename.c_str());
}
/// \brief Prefix of the input state file
inline std::string & input_prefix()
{

2
lib/colvars/colvars_version.h
View File

@ -1,5 +1,5 @@
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2019-04-26"
#define COLVARS_VERSION "2019-08-01"
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars

8
src/KOKKOS/kokkos.cpp
View File

@ -208,6 +208,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
MPI_Comm_size(world,&nmpi);
if (nmpi > 0) {
#if defined(MPI_VERSION) && (MPI_VERSION > 2)
// Check for IBM Spectrum MPI
int len;
@ -226,6 +227,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (me == 0)
error->warning(FLERR,"The Spectrum MPI '-gpu' flag is not set. Disabling CUDA-aware MPI");
}
#endif
if (cuda_aware_flag == 1 && have_cuda_aware == 0) {
if (me == 0)
@ -234,10 +236,10 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
cuda_aware_flag = 0;
} else if (have_cuda_aware == -1) { // maybe we are dealing with MPICH, MVAPICH2 or some derivative?
// MVAPICH2
#if (defined MPICH) && (defined MVAPICH2_VERSION)
#if defined(MPICH) && defined(MVAPICH2_VERSION)
char* str;
cuda_aware_flag = 0;
if (str = getenv("MV2_ENABLE_CUDA")
if ((str = getenv("MV2_ENABLE_CUDA")))
if ((strcmp(str,"1") == 0))
cuda_aware_flag = 1;
@ -245,7 +247,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (me == 0)
error->warning(FLERR,"MVAPICH2 'MV2_ENABLE_CUDA' environment variable is not set. Disabling CUDA-aware MPI");
// pure MPICH or some unsupported MPICH derivative
#elif (defined MPICH) && !(defined MVAPICH2_VERSION)
#elif defined(MPICH) && !defined(MVAPICH2_VERSION)
if (me == 0)
error->warning(FLERR,"Detected MPICH. Disabling CUDA-aware MPI");
cuda_aware_flag = 0;

42
src/REPLICA/temper.cpp
View File

@ -31,6 +31,7 @@
#include "finish.h"
#include "timer.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -70,6 +71,10 @@ void Temper::command(int narg, char **arg)
nevery = force->inumeric(FLERR,arg[1]);
double temp = force->numeric(FLERR,arg[2]);
// ignore temper command, if walltime limit was already reached
if (timer->is_timeout()) return;
for (whichfix = 0; whichfix < modify->nfix; whichfix++)
if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
if (whichfix == modify->nfix)
@ -94,39 +99,18 @@ void Temper::command(int narg, char **arg)
// fix style must be appropriate for temperature control, i.e. it needs
// to provide a working Fix::reset_target() and must not change the volume.
if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/asphere") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/asphere/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/body") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/eff") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/intel") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/kk") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/kk/host") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/kk/device") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/sphere") != 0) &&
(strcmp(modify->fix[whichfix]->style,"nvt/sphere/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin/drude") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin/eff") != 0) &&
(strcmp(modify->fix[whichfix]->style,"gld") != 0) &&
(strcmp(modify->fix[whichfix]->style,"gle") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt/small") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"rigid/nvt/small/omp") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/berendsen/cuda") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/csvr") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/csld") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale/cuda") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale/eff") != 0))
if ((!utils::strmatch(modify->fix[whichfix]->style,"^nvt")) &&
(!utils::strmatch(modify->fix[whichfix]->style,"^langevin")) &&
(!utils::strmatch(modify->fix[whichfix]->style,"^gl[de]$")) &&
(!utils::strmatch(modify->fix[whichfix]->style,"^rigid/nvt")) &&
(!utils::strmatch(modify->fix[whichfix]->style,"^temp/")))
error->universe_all(FLERR,"Tempering temperature fix is not supported");
// setup for long tempering run
update->whichflag = 1;
timer->init_timeout();
update->nsteps = nsteps;
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
@ -233,7 +217,9 @@ void Temper::command(int narg, char **arg)
// run for nevery timesteps
timer->init_timeout();
update->integrate->run(nevery);
if (timer->is_timeout()) break;
// compute PE
// notify compute it will be called at next swap

76
src/USER-BOCS/fix_bocs.cpp
View File

@ -59,6 +59,9 @@ enum{NOBIAS,BIAS};
enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO,TRICLINIC};
// NB: Keep error and warning messages less than 255 chars long.
const int MAX_MESSAGE_LENGTH = 256;
/* ----------------------------------------------------------------------
NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
---------------------------------------------------------------------- */
@ -630,24 +633,32 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
double **data = (double **) calloc(N_columns,sizeof(double *));
char * line = (char *) calloc(200,sizeof(char));
bool badInput = false;
char badDataMsg[MAX_MESSAGE_LENGTH];
fpi = fopen(filename,"r");
if (fpi)
{
while (fgets(line,199,fpi)) { ++n_entries; }
fclose(fpi);
for (i = 0; i < N_columns; ++i)
{
data[i] = (double *) calloc(n_entries,sizeof(double));
}
} else {
char errmsg[128];
snprintf(errmsg,128,"Unable to open file: %s\n",filename);
error->all(FLERR,errmsg);
}
n_entries = 0;
fpi = fopen(filename,"r");
if (fpi) {
// Don't need to re-open the file to make a second pass through it
// simply rewind to beginning
rewind(fpi);
double stdVolumeInterval = 0.0;
double currVolumeInterval = 0.0;
// When comparing doubles/floats, we need an Epsilon.
// The literature indicates getting this value right in the
// general case can be pretty complicated. I don't think it
// needs to be complicated here, though. At least based on the
// sample data I've seen where the volume values are fairly
// large.
const double volumeIntervalTolerance = 0.001;
n_entries = 0;
while( fgets(line,199,fpi)) {
++n_entries;
test_sscanf = sscanf(line," %f , %f ",&f1, &f2);
@ -655,19 +666,47 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
{
data[0][n_entries-1] = (double) f1;
data[1][n_entries-1] = (double) f2;
if (n_entries == 2) {
stdVolumeInterval = data[0][n_entries-1] - data[0][n_entries-2];
}
else if (n_entries > 2) {
currVolumeInterval = data[0][n_entries-1] - data[0][n_entries-2];
if (fabs(currVolumeInterval - stdVolumeInterval) > volumeIntervalTolerance) {
snprintf(badDataMsg,MAX_MESSAGE_LENGTH,
"BAD VOLUME INTERVAL: spline analysis requires uniform"
" volume distribution, found inconsistent volume"
" differential, line %d of file %s\n\tline: %s",
n_entries,filename,line);
error->message(FLERR,badDataMsg);
badInput = true;
}
}
// no else -- first entry is simply ignored
}
else
{
fprintf(stderr,"WARNING: did not find 2 comma separated values in "
"line %d of file %s\n\tline: %s",n_entries,filename,line);
snprintf(badDataMsg,MAX_MESSAGE_LENGTH,
"BAD INPUT FORMAT: did not find 2 comma separated numeric"
" values in line %d of file %s\n\tline: %s",
n_entries,filename,line);
error->message(FLERR,badDataMsg);
badInput = true;
}
}
} else {
char errmsg[128];
snprintf(errmsg,128,"Unable to open file: %s\n",filename);
fclose(fpi);
}
else {
char errmsg[MAX_MESSAGE_LENGTH];
snprintf(errmsg,MAX_MESSAGE_LENGTH,"Unable to open file: %s\n",filename);
error->all(FLERR,errmsg);
}
if (badInput) {
char errmsg[MAX_MESSAGE_LENGTH];
snprintf(errmsg,MAX_MESSAGE_LENGTH,
"Bad volume / pressure-correction data: %s\nSee details above",filename);
error->all(FLERR,errmsg);
}
fclose(fpi);
if (p_basis_type == 1)
{
@ -691,9 +730,10 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
}
else
{
char * errmsg = (char *) calloc(70,sizeof(char));
sprintf(errmsg,"ERROR: invalid p_basis_type value "
"of %d in read_F_table",p_basis_type);
char errmsg[MAX_MESSAGE_LENGTH];
snprintf(errmsg, MAX_MESSAGE_LENGTH,
"ERROR: invalid p_basis_type value of %d in read_F_table",
p_basis_type);
error->all(FLERR,errmsg);
}
// cleanup

2
src/USER-COLVARS/colvarproxy_lammps_version.h
View File

@ -1,5 +1,5 @@
#ifndef COLVARPROXY_VERSION
#define COLVARPROXY_VERSION "2019-04-09"
#define COLVARPROXY_VERSION "2019-08-01"
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars

6
src/USER-INTEL/fix_intel.cpp
View File

@ -352,15 +352,15 @@ void FixIntel::init()
if (_offload_balance != 0.0) off_mode = 1;
if (_precision_mode == PREC_MODE_SINGLE) {
_single_buffers->zero_ev();
_single_buffers->grow_ncache(off_mode,_nthreads);
_single_buffers->grow_ncache(off_mode, comm->nthreads);
_single_buffers->free_list_ptrs();
} else if (_precision_mode == PREC_MODE_MIXED) {
_mixed_buffers->zero_ev();
_mixed_buffers->grow_ncache(off_mode,_nthreads);
_mixed_buffers->grow_ncache(off_mode, comm->nthreads);
_mixed_buffers->free_list_ptrs();
} else {
_double_buffers->zero_ev();
_double_buffers->grow_ncache(off_mode,_nthreads);
_double_buffers->grow_ncache(off_mode, comm->nthreads);
_double_buffers->free_list_ptrs();
}

4
src/USER-INTEL/intel_intrinsics_airebo.h
View File

@ -2223,7 +2223,9 @@ public:
}
VEC_INLINE static ivec unpackloepi32(const fvec &a) {
return reinterpret_cast<const int*>(&a.val_)[0];
union { int i; flt_t f; } atype;
atype.f = a.val_;
return ivec(atype.i);
}
VEC_INLINE static fvec mask_sincos(

1
src/USER-INTEL/pair_eam_intel.cpp
View File

@ -451,7 +451,6 @@ void PairEAMIntel::eval(const int offload, const int vflag,
if (tid == 0)
comm->forward_comm_pair(this);
if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T));
#if defined(_OPENMP)
#pragma omp barrier

1424
src/USER-MISC/pair_ilp_graphene_hbn.cpp
View File

File diff suppressed because it is too large Load Diff

6
src/USER-MISC/pair_ilp_graphene_hbn.h
View File

@ -34,9 +34,10 @@ class PairILPGrapheneHBN : public Pair {
void coeff(int, char **);
double init_one(int, int);
void init_style();
void ILP_neigh();
void calc_normal();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
void calc_FRep(int, int);
void calc_FvdW(int, int);
double single(int, int, int, int, double, double, double, double &);
protected:
@ -74,7 +75,6 @@ class PairILPGrapheneHBN : public Pair {
void read_file( char * );
void allocate();
void ILP_neigh();
/* ----Calculate the long-range cutoff term */
inline double calc_Tap(double r_ij, double Rcut) {

1438
src/USER-MISC/pair_kolmogorov_crespi_full.cpp
View File

File diff suppressed because it is too large Load Diff

6
src/USER-MISC/pair_kolmogorov_crespi_full.h
View File

@ -34,9 +34,10 @@ class PairKolmogorovCrespiFull : public Pair {
void coeff(int, char **);
double init_one(int, int);
void init_style();
void KC_neigh();
void calc_normal();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
void calc_FRep(int, int);
void calc_FvdW(int, int);
double single(int, int, int, int, double, double, double, double &);
protected:
@ -75,7 +76,6 @@ class PairKolmogorovCrespiFull : public Pair {
void read_file( char * );
void allocate();
void KC_neigh();
/* ----Calculate the long-range cutoff term */

8
src/USER-MISC/temper_grem.cpp
View File

@ -71,6 +71,9 @@ void TemperGrem::command(int narg, char **arg)
nevery = force->inumeric(FLERR,arg[1]);
double lambda = force->numeric(FLERR,arg[2]);
// ignore temper command, if walltime limit was already reached
if (timer->is_timeout()) return;
// Get and check if gREM fix exists
for (whichfix = 0; whichfix < modify->nfix; whichfix++)
if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
@ -127,6 +130,8 @@ void TemperGrem::command(int narg, char **arg)
// setup for long tempering run
update->whichflag = 1;
timer->init_timeout();
update->nsteps = nsteps;
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
@ -234,7 +239,9 @@ void TemperGrem::command(int narg, char **arg)
// run for nevery timesteps
timer->init_timeout();
update->integrate->run(nevery);
if (timer->is_timeout()) break;
// compute PE
// notify compute it will be called at next swap
@ -242,7 +249,6 @@ void TemperGrem::command(int narg, char **arg)
pe = pe_compute->compute_scalar();
pe_compute->addstep(update->ntimestep + nevery);
// which = which of 2 kinds of swaps to do (0,1)
if (!ranswap) which = iswap % 2;

13
src/USER-MISC/temper_npt.cpp
View File

@ -33,6 +33,7 @@
#include "finish.h"
#include "timer.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -73,6 +74,10 @@ void TemperNPT::command(int narg, char **arg)
double temp = force->numeric(FLERR,arg[2]);
double press_set = force->numeric(FLERR,arg[6]);
// ignore temper command, if walltime limit was already reached
if (timer->is_timeout()) return;
for (whichfix = 0; whichfix < modify->nfix; whichfix++)
if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
if (whichfix == modify->nfix)
@ -97,13 +102,15 @@ void TemperNPT::command(int narg, char **arg)
// change the volume. This currently only applies to fix npt and
// fix rigid/npt variants
if ((strncmp(modify->fix[whichfix]->style,"npt",3) != 0)
&& (strncmp(modify->fix[whichfix]->style,"rigid/npt",9) != 0))
if ( (!utils::strmatch(modify->fix[whichfix]->style,"^npt")) &&
(!utils::strmatch(modify->fix[whichfix]->style,"^rigid/npt")) )
error->universe_all(FLERR,"Tempering temperature and pressure fix is not supported");
// setup for long tempering run
update->whichflag = 1;
timer->init_timeout();
update->nsteps = nsteps;
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
@ -211,7 +218,9 @@ void TemperNPT::command(int narg, char **arg)
// run for nevery timesteps
timer->init_timeout();
update->integrate->run(nevery);
if (timer->is_timeout()) break;
// compute PE
// notify compute it will be called at next swap

4
src/USER-OMP/thr_data.h
View File

@ -31,7 +31,7 @@ class ThrData {
public:
ThrData(int tid, class Timer *t);
~ThrData() { delete _timer; _timer = nullptr; };
~ThrData() { delete _timer; _timer = NULL; };
void check_tid(int); // thread id consistency check
int get_tid() const { return _tid; }; // our thread id.
@ -136,7 +136,7 @@ class ThrData {
// disabled default methods
private:
ThrData() : _tid(-1), _timer(nullptr) {};
ThrData() : _tid(-1), _timer(NULL) {};
};
////////////////////////////////////////////////////////////////////////

2
src/USER-PHONON/Install.sh
View File

@ -42,5 +42,3 @@ action fix_phonon.cpp fft3d_wrap.h
action fix_phonon.h fft3d_wrap.h
action dynamical_matrix.cpp
action dynamical_matrix.h
action third_order.cpp
action third_order.h

1
src/USER-PTM/ptm_initialize_data.h
View File

@ -15,6 +15,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
#include "ptm_deformation_gradient.h"
#include "ptm_fundamental_mappings.h"
#include "ptm_alt_templates.h"
#include <cstddef>
namespace ptm {

4
src/error.cpp
View File

@ -19,6 +19,10 @@
#include "output.h"
#include "input.h"
#if defined(LAMMPS_EXCEPTIONS)
#include "update.h"
#endif
using namespace LAMMPS_NS;
// helper function to truncate a string to a segment starting with "src/";

7
src/info.cpp
View File

@ -354,10 +354,15 @@ void Info::command(int narg, char **arg)
if (flags & COMM) {
int major,minor,len;
#if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS)
char version[MPI_MAX_LIBRARY_VERSION_STRING];
MPI_Get_library_version(version,&len);
#else
char version[] = "Undetected MPI implementation";
len = strlen(version);
#endif
MPI_Get_version(&major,&minor);
MPI_Get_library_version(version,&len);
if (len > 80) {
char *ptr = strchr(version+80,'\n');
if (ptr) *ptr = '\0';

29
src/library.cpp
View File

@ -38,6 +38,10 @@
#include "force.h"
#include "info.h"
#if defined(LAMMPS_EXCEPTIONS)
#include "exceptions.h"
#endif
using namespace LAMMPS_NS;
// ----------------------------------------------------------------------
@ -806,7 +810,10 @@ void lammps_gather_atoms(void *ptr, char * /*name */,
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
lmp->error->all(FLERR,"Library function lammps_gather_atoms() not compatible with -DLAMMPS_BIGBIG");
{
lmp->error->all(FLERR,"Library function lammps_gather_atoms() "
"is not compatible with -DLAMMPS_BIGBIG");
}
END_CAPTURE
}
#else
@ -944,7 +951,10 @@ void lammps_gather_atoms_concat(void *ptr, char * /*name */,
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
lmp->error->all(FLERR,"Library function lammps_gather_atoms_concat() not compatible with -DLAMMPS_BIGBIG");
{
lmp->error->all(FLERR,"Library function lammps_gather_atoms_concat() "
"is not compatible with -DLAMMPS_BIGBIG");
}
END_CAPTURE
}
#else
@ -1101,7 +1111,10 @@ void lammps_gather_atoms_subset(void *ptr, char * /*name */,
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
lmp->error->all(FLERR,"Library function lammps_gather_atoms_subset() not compatible with -DLAMMPS_BIGBIG");
{
lmp->error->all(FLERR,"Library function lammps_gather_atoms_subset() "
"is not compatible with -DLAMMPS_BIGBIG");
}
END_CAPTURE
}
#else
@ -1247,7 +1260,10 @@ void lammps_scatter_atoms(void *ptr, char * /*name */,
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
lmp->error->all(FLERR,"Library function lammps_scatter_atoms() not compatible with -DLAMMPS_BIGBIG");
{
lmp->error->all(FLERR,"Library function lammps_scatter_atoms() "
"is not compatible with -DLAMMPS_BIGBIG");
}
END_CAPTURE
}
#else
@ -1373,7 +1389,10 @@ void lammps_scatter_atoms_subset(void *ptr, char * /*name */,
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
lmp->error->all(FLERR,"Library function lammps_scatter_atoms_subset() not compatible with -DLAMMPS_BIGBIG");
{
lmp->error->all(FLERR,"Library function lammps_scatter_atoms_subset() "
"is not compatible with -DLAMMPS_BIGBIG");
}
END_CAPTURE
}
#else

4
src/main.cpp
View File

@ -23,6 +23,10 @@
#include <fftw3.h>
#endif
#if defined(LAMMPS_EXCEPTIONS)
#include "exceptions.h"
#endif
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "31 Jul 2019"
#define LAMMPS_VERSION "2 Aug 2019"