From 3e60f79f1d6256a1bfd346b52bbd59095e751ec3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 26 Apr 2017 17:24:25 -0400 Subject: [PATCH 1/7] remove cg/cmm style name aliases --- src/GPU/pair_lj_sdk_coul_long_gpu.h | 1 - src/GPU/pair_lj_sdk_gpu.h | 1 - src/USER-CG-CMM/angle_sdk.h | 1 - src/USER-CG-CMM/pair_lj_sdk.h | 1 - src/USER-CG-CMM/pair_lj_sdk_coul_long.h | 1 - src/USER-CG-CMM/pair_lj_sdk_coul_msm.h | 1 - src/USER-OMP/angle_sdk_omp.h | 1 - src/USER-OMP/pair_lj_sdk_coul_long_omp.h | 1 - src/USER-OMP/pair_lj_sdk_coul_msm_omp.h | 3 +-- src/USER-OMP/pair_lj_sdk_omp.h | 1 - 10 files changed, 1 insertion(+), 11 deletions(-) diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.h b/src/GPU/pair_lj_sdk_coul_long_gpu.h index 61de272979..3248e94977 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.h +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.h @@ -14,7 +14,6 @@ #ifdef PAIR_CLASS PairStyle(lj/sdk/coul/long/gpu,PairLJSDKCoulLongGPU) -PairStyle(cg/cmm/coul/long/gpu,PairLJSDKCoulLongGPU) #else diff --git a/src/GPU/pair_lj_sdk_gpu.h b/src/GPU/pair_lj_sdk_gpu.h index 610fb8b0e4..3865b34046 100644 --- a/src/GPU/pair_lj_sdk_gpu.h +++ b/src/GPU/pair_lj_sdk_gpu.h @@ -14,7 +14,6 @@ #ifdef PAIR_CLASS PairStyle(lj/sdk/gpu,PairLJSDKGPU) -PairStyle(cg/cmm/gpu,PairLJSDKGPU) #else diff --git a/src/USER-CG-CMM/angle_sdk.h b/src/USER-CG-CMM/angle_sdk.h index fbd5461187..a5d917e57c 100644 --- a/src/USER-CG-CMM/angle_sdk.h +++ b/src/USER-CG-CMM/angle_sdk.h @@ -14,7 +14,6 @@ #ifdef ANGLE_CLASS AngleStyle(sdk,AngleSDK) -AngleStyle(cg/cmm,AngleSDK) #else diff --git a/src/USER-CG-CMM/pair_lj_sdk.h b/src/USER-CG-CMM/pair_lj_sdk.h index de27485c14..ef0263c06b 100644 --- a/src/USER-CG-CMM/pair_lj_sdk.h +++ b/src/USER-CG-CMM/pair_lj_sdk.h @@ -18,7 +18,6 @@ #ifdef PAIR_CLASS PairStyle(lj/sdk,PairLJSDK) -PairStyle(cg/cmm,PairLJSDK) #else diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_long.h b/src/USER-CG-CMM/pair_lj_sdk_coul_long.h index 508ffe5e6d..57779cc0b9 100644 --- a/src/USER-CG-CMM/pair_lj_sdk_coul_long.h +++ b/src/USER-CG-CMM/pair_lj_sdk_coul_long.h @@ -18,7 +18,6 @@ #ifdef PAIR_CLASS PairStyle(lj/sdk/coul/long,PairLJSDKCoulLong) -PairStyle(cg/cmm/coul/long,PairLJSDKCoulLong) #else diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_msm.h b/src/USER-CG-CMM/pair_lj_sdk_coul_msm.h index be56c0cec3..8438ced66b 100644 --- a/src/USER-CG-CMM/pair_lj_sdk_coul_msm.h +++ b/src/USER-CG-CMM/pair_lj_sdk_coul_msm.h @@ -18,7 +18,6 @@ #ifdef PAIR_CLASS PairStyle(lj/sdk/coul/msm,PairLJSDKCoulMSM) -PairStyle(cg/cmm/coul/msm,PairLJSDKCoulMSM) #else diff --git a/src/USER-OMP/angle_sdk_omp.h b/src/USER-OMP/angle_sdk_omp.h index 9ab75904ce..c041c2ecc2 100644 --- a/src/USER-OMP/angle_sdk_omp.h +++ b/src/USER-OMP/angle_sdk_omp.h @@ -18,7 +18,6 @@ #ifdef ANGLE_CLASS AngleStyle(sdk/omp,AngleSDKOMP) -AngleStyle(cg/cmm/omp,AngleSDKOMP) #else diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.h b/src/USER-OMP/pair_lj_sdk_coul_long_omp.h index a615efb507..1886d2c7b5 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.h +++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.h @@ -18,7 +18,6 @@ #ifdef PAIR_CLASS PairStyle(lj/sdk/coul/long/omp,PairLJSDKCoulLongOMP) -PairStyle(cg/cmm/coul/long/omp,PairLJSDKCoulLongOMP) #else diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h index 9e4a922c39..9841408b8a 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h +++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.h @@ -18,7 +18,6 @@ #ifdef PAIR_CLASS PairStyle(lj/sdk/coul/msm/omp,PairLJSDKCoulMSMOMP) -PairStyle(cg/cmm/coul/msm/omp,PairLJSDKCoulMSMOMP) #else @@ -54,4 +53,4 @@ E: Must use 'kspace_modify pressure/scalar no' with OMP MSM Pair styles The kspace scalar pressure option is not (yet) compatible with OMP MSM Pair styles. -*/ \ No newline at end of file +*/ diff --git a/src/USER-OMP/pair_lj_sdk_omp.h b/src/USER-OMP/pair_lj_sdk_omp.h index c3837fb683..36c913252a 100644 --- a/src/USER-OMP/pair_lj_sdk_omp.h +++ b/src/USER-OMP/pair_lj_sdk_omp.h @@ -18,7 +18,6 @@ #ifdef PAIR_CLASS PairStyle(lj/sdk/omp,PairLJSDKOMP) -PairStyle(cg/cmm/omp,PairLJSDKOMP) #else From 949d61e01edad9a8ea056ccbc21c5fe21a87bafc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 26 Apr 2017 19:26:27 -0400 Subject: [PATCH 2/7] rename examples folder for USER-CGSDK package --- examples/USER/{cg-cmm => cgsdk}/README | 2 +- .../{cg-cmm => cgsdk}/peg-verlet/data.pegc12e8.gz | Bin .../USER/{cg-cmm => cgsdk}/peg-verlet/in.pegc12e8 | 0 .../{cg-cmm => cgsdk}/peg-verlet/in.pegc12e8-angle | 0 .../USER/{cg-cmm => cgsdk}/peg-verlet/log.pegc12e8 | 0 .../{cg-cmm => cgsdk}/peg-verlet/log.pegc12e8-angle | 0 .../{cg-cmm => cgsdk}/sds-monolayer/data.sds.gz | Bin .../{cg-cmm => cgsdk}/sds-monolayer/in.sds-hybrid | 0 .../{cg-cmm => cgsdk}/sds-monolayer/in.sds-regular | 0 .../{cg-cmm => cgsdk}/sds-monolayer/log.sds-hybrid | 0 .../{cg-cmm => cgsdk}/sds-monolayer/log.sds-regular | 0 11 files changed, 1 insertion(+), 1 deletion(-) rename examples/USER/{cg-cmm => cgsdk}/README (95%) rename examples/USER/{cg-cmm => cgsdk}/peg-verlet/data.pegc12e8.gz (100%) rename examples/USER/{cg-cmm => cgsdk}/peg-verlet/in.pegc12e8 (100%) rename examples/USER/{cg-cmm => cgsdk}/peg-verlet/in.pegc12e8-angle (100%) rename examples/USER/{cg-cmm => cgsdk}/peg-verlet/log.pegc12e8 (100%) rename examples/USER/{cg-cmm => cgsdk}/peg-verlet/log.pegc12e8-angle (100%) rename examples/USER/{cg-cmm => cgsdk}/sds-monolayer/data.sds.gz (100%) rename examples/USER/{cg-cmm => cgsdk}/sds-monolayer/in.sds-hybrid (100%) rename examples/USER/{cg-cmm => cgsdk}/sds-monolayer/in.sds-regular (100%) rename examples/USER/{cg-cmm => cgsdk}/sds-monolayer/log.sds-hybrid (100%) rename examples/USER/{cg-cmm => cgsdk}/sds-monolayer/log.sds-regular (100%) diff --git a/examples/USER/cg-cmm/README b/examples/USER/cgsdk/README similarity index 95% rename from examples/USER/cg-cmm/README rename to examples/USER/cgsdk/README index 6a283114ba..5d3a493779 100644 --- a/examples/USER/cg-cmm/README +++ b/examples/USER/cgsdk/README @@ -1,4 +1,4 @@ -LAMMPS USER-CMM-CG example problems +LAMMPS USER-CGSDK example problems Each of these sub-directories contains a sample problem for the SDK coarse grained MD potentials that you can run with LAMMPS. diff --git a/examples/USER/cg-cmm/peg-verlet/data.pegc12e8.gz b/examples/USER/cgsdk/peg-verlet/data.pegc12e8.gz similarity index 100% rename from examples/USER/cg-cmm/peg-verlet/data.pegc12e8.gz rename to examples/USER/cgsdk/peg-verlet/data.pegc12e8.gz diff --git a/examples/USER/cg-cmm/peg-verlet/in.pegc12e8 b/examples/USER/cgsdk/peg-verlet/in.pegc12e8 similarity index 100% rename from examples/USER/cg-cmm/peg-verlet/in.pegc12e8 rename to examples/USER/cgsdk/peg-verlet/in.pegc12e8 diff --git a/examples/USER/cg-cmm/peg-verlet/in.pegc12e8-angle b/examples/USER/cgsdk/peg-verlet/in.pegc12e8-angle similarity index 100% rename from examples/USER/cg-cmm/peg-verlet/in.pegc12e8-angle rename to examples/USER/cgsdk/peg-verlet/in.pegc12e8-angle diff --git a/examples/USER/cg-cmm/peg-verlet/log.pegc12e8 b/examples/USER/cgsdk/peg-verlet/log.pegc12e8 similarity index 100% rename from examples/USER/cg-cmm/peg-verlet/log.pegc12e8 rename to examples/USER/cgsdk/peg-verlet/log.pegc12e8 diff --git a/examples/USER/cg-cmm/peg-verlet/log.pegc12e8-angle b/examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle similarity index 100% rename from examples/USER/cg-cmm/peg-verlet/log.pegc12e8-angle rename to examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle diff --git a/examples/USER/cg-cmm/sds-monolayer/data.sds.gz b/examples/USER/cgsdk/sds-monolayer/data.sds.gz similarity index 100% rename from examples/USER/cg-cmm/sds-monolayer/data.sds.gz rename to examples/USER/cgsdk/sds-monolayer/data.sds.gz diff --git a/examples/USER/cg-cmm/sds-monolayer/in.sds-hybrid b/examples/USER/cgsdk/sds-monolayer/in.sds-hybrid similarity index 100% rename from examples/USER/cg-cmm/sds-monolayer/in.sds-hybrid rename to examples/USER/cgsdk/sds-monolayer/in.sds-hybrid diff --git a/examples/USER/cg-cmm/sds-monolayer/in.sds-regular b/examples/USER/cgsdk/sds-monolayer/in.sds-regular similarity index 100% rename from examples/USER/cg-cmm/sds-monolayer/in.sds-regular rename to examples/USER/cgsdk/sds-monolayer/in.sds-regular diff --git a/examples/USER/cg-cmm/sds-monolayer/log.sds-hybrid b/examples/USER/cgsdk/sds-monolayer/log.sds-hybrid similarity index 100% rename from examples/USER/cg-cmm/sds-monolayer/log.sds-hybrid rename to examples/USER/cgsdk/sds-monolayer/log.sds-hybrid diff --git a/examples/USER/cg-cmm/sds-monolayer/log.sds-regular b/examples/USER/cgsdk/sds-monolayer/log.sds-regular similarity index 100% rename from examples/USER/cg-cmm/sds-monolayer/log.sds-regular rename to examples/USER/cgsdk/sds-monolayer/log.sds-regular From af748745162c73b51153a399a63e2811e55da536 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 26 Apr 2017 19:27:13 -0400 Subject: [PATCH 3/7] rename references to USER-CG-CMM to USER-CGSDK --- doc/src/Section_intro.txt | 2 +- doc/src/Section_packages.txt | 32 +++++++++++++++++--------------- doc/src/angle_sdk.txt | 2 +- doc/src/pair_sdk.txt | 2 +- 4 files changed, 20 insertions(+), 18 deletions(-) diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt index 33c3cf395f..0c438c6ce0 100644 --- a/doc/src/Section_intro.txt +++ b/doc/src/Section_intro.txt @@ -515,7 +515,7 @@ the packages they have written are somewhat unique to LAMMPS and the code would not be as general-purpose as it is without their expertise and efforts. -Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages +Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK and USER-OMP packages Roy Pollock (LLNL), Ewald and PPPM solvers Mike Brown (ORNL), brownw at ornl.gov, GPU package Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index b327b7b1ce..bd81361fa9 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -1139,8 +1139,8 @@ The current list of user-contributed packages is as follows: Package, Description, Author(s), Doc page, Example, Pic/movie, Library "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd -"USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, - "USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Strathclyde Glasgow), src/USER-CGDNA/README, USER/cgdna, -, - +"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, "cgsdk"_cgsdk, - "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, - "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, - @@ -1169,7 +1169,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library :tb(ea=c) :link(atc,http://lammps.sandia.gov/pictures.html#atc) -:link(cg,http://lammps.sandia.gov/pictures.html#cg) +:link(cgsdk,http://lammps.sandia.gov/pictures.html#cg) :link(eff,http://lammps.sandia.gov/movies.html#eff) :link(manifold,http://lammps.sandia.gov/movies.html#manifold) :link(sph,http://lammps.sandia.gov/movies.html#sph) @@ -1267,18 +1267,18 @@ physik.hu-berlin.de). Contact him directly if you have questions. :line -USER-CG-CMM package :link(USER-CG-CMM),h5 +USER-CGSDK package :link(USER-CGSDK),h5 -Contents: CG-CMM stands for coarse-grained ??. This package -implements several pair styles and an angle style using the coarse -grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 -(2007) (SDK), with extensions to simulate ionic liquids, electrolytes, -lipids and charged amino acids. See src/USER-CG-CMM/README for more -details. +Contents: CGSDK stands for Shinoda-DeVane-Klein (SDK) coarse-grained +molecular dynamics force field. This package implements several pair +styles and an angle style using the coarse grained parametrization of +Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) (SDK), with extensions +to simulate ionic liquids, electrolytes, lipids and charged amino acids. +See src/USER-CGSDK/README for more details. -Supporting info: src/USER-CG-CMM/README, "pair lj/sdk"_pair_sdk.html, +Supporting info: src/USER-CGSDK/README, "pair lj/sdk"_pair_sdk.html, "pair lj/sdk/coul/long"_pair_sdk.html, "angle sdk"_angle_sdk.html, -examples/USER/cg-cmm +examples/USER/cgsdk Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. @@ -1329,10 +1329,12 @@ src/USER-COLVARS/README, lib/colvars/README, "fix colvars"_fix_colvars.html, examples/USER/colvars Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the -fix. The COLVARS library itself is written and maintained by Giacomo -Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome -Henin (LISM, CNRS, Marseille, France). Contact them directly if you -have questions. +interface that integrates colvars into LAMMPS. The COLVARS library +itself is written and maintained by Giacomo Fiorin (ICMS, Temple +University, Philadelphia, PA, USA) and Jerome Henin (LISM, CNRS, +Marseille, France). For more info, and to communicate with the COLVARS +developers, please go to COLVARS home page at +"http://colvars.github.io"_http://colvars.github.io/. :line diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt index 785585f840..0cc535e543 100644 --- a/doc/src/angle_sdk.txt +++ b/doc/src/angle_sdk.txt @@ -46,7 +46,7 @@ from the pair_style. [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER-CG-CMM package. See the "Making +USER-CGSDK package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index 212760e03d..1c348eaaf7 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -134,7 +134,7 @@ respa"_run_style.html command. [Restrictions:] -All of the lj/sdk pair styles are part of the USER-CG-CMM package. +All of the lj/sdk pair styles are part of the USER-CGSDK package. The {lj/sdk/coul/long} style also requires the KSPACE package to be built (which is enabled by default). They are only enabled if LAMMPS was built with that package. See the "Making From 5c7a63198832e6864288e7087376e035f3c18244 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 26 Apr 2017 19:29:39 -0400 Subject: [PATCH 4/7] rename USER-CG-CMM folder to USER-CGSDK --- src/Depend.sh | 2 +- src/Makefile | 2 +- src/{USER-CG-CMM => USER-CGSDK}/Install.sh | 0 src/{USER-CG-CMM => USER-CGSDK}/README | 0 src/{USER-CG-CMM => USER-CGSDK}/angle_sdk.cpp | 0 src/{USER-CG-CMM => USER-CGSDK}/angle_sdk.h | 0 src/{USER-CG-CMM => USER-CGSDK}/lj_sdk_common.h | 0 src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk.cpp | 0 src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk.h | 0 src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk_coul_long.cpp | 0 src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk_coul_long.h | 0 src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk_coul_msm.cpp | 0 src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk_coul_msm.h | 0 13 files changed, 2 insertions(+), 2 deletions(-) rename src/{USER-CG-CMM => USER-CGSDK}/Install.sh (100%) rename src/{USER-CG-CMM => USER-CGSDK}/README (100%) rename src/{USER-CG-CMM => USER-CGSDK}/angle_sdk.cpp (100%) rename src/{USER-CG-CMM => USER-CGSDK}/angle_sdk.h (100%) rename src/{USER-CG-CMM => USER-CGSDK}/lj_sdk_common.h (100%) rename src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk.cpp (100%) rename src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk.h (100%) rename src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk_coul_long.cpp (100%) rename src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk_coul_long.h (100%) rename src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk_coul_msm.cpp (100%) rename src/{USER-CG-CMM => USER-CGSDK}/pair_lj_sdk_coul_msm.h (100%) diff --git a/src/Depend.sh b/src/Depend.sh index 5a48a7c163..520d9ae2bf 100644 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -109,7 +109,7 @@ if (test $1 = "RIGID") then depend USER-OMP fi -if (test $1 = "USER-CG-CMM") then +if (test $1 = "USER-CGSDK") then depend GPU depend KOKKOS depend USER-OMP diff --git a/src/Makefile b/src/Makefile index e6821646d1..527e197964 100644 --- a/src/Makefile +++ b/src/Makefile @@ -57,7 +57,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ mpiio mscg opt peri poems \ python qeq reax replica rigid shock snap srd voronoi -PACKUSER = user-atc user-awpmd user-cg-cmm user-cgdna user-colvars \ +PACKUSER = user-atc user-awpmd user-cgsdk user-cgdna user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-mgpt user-misc user-molfile \ user-nc-dump user-omp user-phonon user-qmmm user-qtb \ diff --git a/src/USER-CG-CMM/Install.sh b/src/USER-CGSDK/Install.sh similarity index 100% rename from src/USER-CG-CMM/Install.sh rename to src/USER-CGSDK/Install.sh diff --git a/src/USER-CG-CMM/README b/src/USER-CGSDK/README similarity index 100% rename from src/USER-CG-CMM/README rename to src/USER-CGSDK/README diff --git a/src/USER-CG-CMM/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp similarity index 100% rename from src/USER-CG-CMM/angle_sdk.cpp rename to src/USER-CGSDK/angle_sdk.cpp diff --git a/src/USER-CG-CMM/angle_sdk.h b/src/USER-CGSDK/angle_sdk.h similarity index 100% rename from src/USER-CG-CMM/angle_sdk.h rename to src/USER-CGSDK/angle_sdk.h diff --git a/src/USER-CG-CMM/lj_sdk_common.h b/src/USER-CGSDK/lj_sdk_common.h similarity index 100% rename from src/USER-CG-CMM/lj_sdk_common.h rename to src/USER-CGSDK/lj_sdk_common.h diff --git a/src/USER-CG-CMM/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp similarity index 100% rename from src/USER-CG-CMM/pair_lj_sdk.cpp rename to src/USER-CGSDK/pair_lj_sdk.cpp diff --git a/src/USER-CG-CMM/pair_lj_sdk.h b/src/USER-CGSDK/pair_lj_sdk.h similarity index 100% rename from src/USER-CG-CMM/pair_lj_sdk.h rename to src/USER-CGSDK/pair_lj_sdk.h diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp similarity index 100% rename from src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp rename to src/USER-CGSDK/pair_lj_sdk_coul_long.cpp diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_long.h b/src/USER-CGSDK/pair_lj_sdk_coul_long.h similarity index 100% rename from src/USER-CG-CMM/pair_lj_sdk_coul_long.h rename to src/USER-CGSDK/pair_lj_sdk_coul_long.h diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp similarity index 100% rename from src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp rename to src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp diff --git a/src/USER-CG-CMM/pair_lj_sdk_coul_msm.h b/src/USER-CGSDK/pair_lj_sdk_coul_msm.h similarity index 100% rename from src/USER-CG-CMM/pair_lj_sdk_coul_msm.h rename to src/USER-CGSDK/pair_lj_sdk_coul_msm.h From 548c589f82d3af95b1865eddb804d6ff00c4ef6a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 26 Apr 2017 19:35:54 -0400 Subject: [PATCH 5/7] update the README for USER-CGSDK --- src/USER-CGSDK/README | 22 +++++++--------------- 1 file changed, 7 insertions(+), 15 deletions(-) diff --git a/src/USER-CGSDK/README b/src/USER-CGSDK/README index b37fbd3760..535bd43ac1 100644 --- a/src/USER-CGSDK/README +++ b/src/USER-CGSDK/README @@ -13,23 +13,15 @@ lipids and charged amino acids. See the doc pages for these commands for details. There are example scripts for using this package in -examples/USER/cg-cmm. +examples/USER/cgsdk This is the second generation implementation reducing the the clutter of the previous version. For many systems with long range electrostatics, it will be faster to use pair_style hybrid/overlay with lj/sdk and coul/long instead of the combined lj/sdk/coul/long -style, since the number of charged atom types is usually small. To -exploit this property, the use of the kspace_style pppm/cg is -recommended over regular pppm. For all new styles, input file backward -compatibility is provided. The old implementation is still available -through appending the /old suffix. These will be discontinued and -removed after the new implementation has been fully validated. - -The current version of this package should be considered beta -quality. The CG potentials work correctly for "normal" situations, but -have not been testing with all kinds of potential parameters and -simuation systems. +style, since the number of charged atom types is usually small. +To exploit this property, the use of the kspace_style pppm/cg is +recommended over regular pppm. The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. @@ -38,9 +30,9 @@ The person who created this package is Axel Kohlmeyer at Temple U Thanks for contributions, support and testing goes to -Wataru Shinoda (AIST, Tsukuba) +Wataru Shinoda (Nagoya University) Russell DeVane (Procter & Gamble) -Michael L. Klein (CMM / U Penn, Philadelphia) +Michael L. Klein (Temple University, Philadelphia) Balasubramanian Sundaram (JNCASR, Bangalore) -version: 0.99 / 2011-11-29 +version: 1.0 / 2017-04-26 From cd435c0c58fe8e89ee1d60266791efbaa3fcba1f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 26 Apr 2017 19:44:25 -0400 Subject: [PATCH 6/7] change references from cg_cmm to lj_sdk and from cmm to sdk --- lib/gpu/Nvidia.makefile | 40 +++++++++++++-------------- lib/gpu/Opencl.makefile | 32 ++++++++++----------- lib/gpu/lal_cg_cmm.cpp | 34 +++++++++++------------ lib/gpu/lal_cg_cmm.cu | 6 ++-- lib/gpu/lal_cg_cmm.h | 4 +-- lib/gpu/lal_cg_cmm_ext.cpp | 14 +++++----- lib/gpu/lal_cg_cmm_long.cpp | 12 ++++---- lib/gpu/lal_cg_cmm_long.cu | 6 ++-- lib/gpu/lal_cg_cmm_long.h | 2 +- lib/gpu/lal_cg_cmm_long_ext.cpp | 14 +++++----- src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 20 +++++++------- src/GPU/pair_lj_sdk_gpu.cpp | 20 +++++++------- 12 files changed, 102 insertions(+), 102 deletions(-) diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile index e02849cfed..660544cfaa 100644 --- a/lib/gpu/Nvidia.makefile +++ b/lib/gpu/Nvidia.makefile @@ -43,8 +43,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \ $(OBJ_DIR)/lal_coul_long.o $(OBJ_DIR)/lal_coul_long_ext.o \ $(OBJ_DIR)/lal_morse.o $(OBJ_DIR)/lal_morse_ext.o \ $(OBJ_DIR)/lal_charmm_long.o $(OBJ_DIR)/lal_charmm_long_ext.o \ - $(OBJ_DIR)/lal_cg_cmm.o $(OBJ_DIR)/lal_cg_cmm_ext.o \ - $(OBJ_DIR)/lal_cg_cmm_long.o $(OBJ_DIR)/lal_cg_cmm_long_ext.o \ + $(OBJ_DIR)/lal_lj_sdk.o $(OBJ_DIR)/lal_lj_sdk_ext.o \ + $(OBJ_DIR)/lal_lj_sdk_long.o $(OBJ_DIR)/lal_lj_sdk_long_ext.o \ $(OBJ_DIR)/lal_eam.o $(OBJ_DIR)/lal_eam_ext.o \ $(OBJ_DIR)/lal_eam_fs_ext.o $(OBJ_DIR)/lal_eam_alloy_ext.o \ $(OBJ_DIR)/lal_buck.o $(OBJ_DIR)/lal_buck_ext.o \ @@ -98,8 +98,8 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/coul_long.cubin $(OBJ_DIR)/coul_long_cubin.h \ $(OBJ_DIR)/morse.cubin $(OBJ_DIR)/morse_cubin.h \ $(OBJ_DIR)/charmm_long.cubin $(OBJ_DIR)/charmm_long_cubin.h \ - $(OBJ_DIR)/cg_cmm.cubin $(OBJ_DIR)/cg_cmm_cubin.h \ - $(OBJ_DIR)/cg_cmm_long.cubin $(OBJ_DIR)/cg_cmm_long_cubin.h \ + $(OBJ_DIR)/lj_sdk.cubin $(OBJ_DIR)/lj_sdk_cubin.h \ + $(OBJ_DIR)/lj_sdk_long.cubin $(OBJ_DIR)/lj_sdk_long_cubin.h \ $(OBJ_DIR)/eam.cubin $(OBJ_DIR)/eam_cubin.h \ $(OBJ_DIR)/buck.cubin $(OBJ_DIR)/buck_cubin.h \ $(OBJ_DIR)/buck_coul_long.cubin $(OBJ_DIR)/buck_coul_long_cubin.h \ @@ -391,29 +391,29 @@ $(OBJ_DIR)/lal_lj_expand.o: $(ALL_H) lal_lj_expand.h lal_lj_expand.cpp $(OBJ_DIR $(OBJ_DIR)/lal_lj_expand_ext.o: $(ALL_H) lal_lj_expand.h lal_lj_expand_ext.cpp lal_base_atomic.h $(CUDR) -o $@ -c lal_lj_expand_ext.cpp -I$(OBJ_DIR) -$(OBJ_DIR)/cg_cmm.cubin: lal_cg_cmm.cu lal_precision.h lal_preprocessor.h - $(CUDA) --cubin -DNV_KERNEL -o $@ lal_cg_cmm.cu +$(OBJ_DIR)/lj_sdk.cubin: lal_lj_sdk.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_sdk.cu -$(OBJ_DIR)/cg_cmm_cubin.h: $(OBJ_DIR)/cg_cmm.cubin $(OBJ_DIR)/cg_cmm.cubin - $(BIN2C) -c -n cg_cmm $(OBJ_DIR)/cg_cmm.cubin > $(OBJ_DIR)/cg_cmm_cubin.h +$(OBJ_DIR)/lj_sdk_cubin.h: $(OBJ_DIR)/lj_sdk.cubin $(OBJ_DIR)/lj_sdk.cubin + $(BIN2C) -c -n lj_sdk $(OBJ_DIR)/lj_sdk.cubin > $(OBJ_DIR)/lj_sdk_cubin.h -$(OBJ_DIR)/lal_cg_cmm.o: $(ALL_H) lal_cg_cmm.h lal_cg_cmm.cpp $(OBJ_DIR)/cg_cmm_cubin.h $(OBJ_DIR)/lal_base_atomic.o - $(CUDR) -o $@ -c lal_cg_cmm.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/lal_lj_sdk.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk.cpp $(OBJ_DIR)/lj_sdk_cubin.h $(OBJ_DIR)/lal_base_atomic.o + $(CUDR) -o $@ -c lal_lj_sdk.cpp -I$(OBJ_DIR) -$(OBJ_DIR)/lal_cg_cmm_ext.o: $(ALL_H) lal_cg_cmm.h lal_cg_cmm_ext.cpp lal_base_atomic.h - $(CUDR) -o $@ -c lal_cg_cmm_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/lal_lj_sdk_ext.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk_ext.cpp lal_base_atomic.h + $(CUDR) -o $@ -c lal_lj_sdk_ext.cpp -I$(OBJ_DIR) -$(OBJ_DIR)/cg_cmm_long.cubin: lal_cg_cmm_long.cu lal_precision.h lal_preprocessor.h - $(CUDA) --cubin -DNV_KERNEL -o $@ lal_cg_cmm_long.cu +$(OBJ_DIR)/lj_sdk_long.cubin: lal_lj_sdk_long.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_sdk_long.cu -$(OBJ_DIR)/cg_cmm_long_cubin.h: $(OBJ_DIR)/cg_cmm_long.cubin $(OBJ_DIR)/cg_cmm_long.cubin - $(BIN2C) -c -n cg_cmm_long $(OBJ_DIR)/cg_cmm_long.cubin > $(OBJ_DIR)/cg_cmm_long_cubin.h +$(OBJ_DIR)/lj_sdk_long_cubin.h: $(OBJ_DIR)/lj_sdk_long.cubin $(OBJ_DIR)/lj_sdk_long.cubin + $(BIN2C) -c -n lj_sdk_long $(OBJ_DIR)/lj_sdk_long.cubin > $(OBJ_DIR)/lj_sdk_long_cubin.h -$(OBJ_DIR)/lal_cg_cmm_long.o: $(ALL_H) lal_cg_cmm_long.h lal_cg_cmm_long.cpp $(OBJ_DIR)/cg_cmm_long_cubin.h $(OBJ_DIR)/lal_base_atomic.o - $(CUDR) -o $@ -c lal_cg_cmm_long.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/lal_lj_sdk_long.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long.cpp $(OBJ_DIR)/lj_sdk_long_cubin.h $(OBJ_DIR)/lal_base_atomic.o + $(CUDR) -o $@ -c lal_lj_sdk_long.cpp -I$(OBJ_DIR) -$(OBJ_DIR)/lal_cg_cmm_long_ext.o: $(ALL_H) lal_cg_cmm_long.h lal_cg_cmm_long_ext.cpp lal_base_charge.h - $(CUDR) -o $@ -c lal_cg_cmm_long_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/lal_lj_sdk_long_ext.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long_ext.cpp lal_base_charge.h + $(CUDR) -o $@ -c lal_lj_sdk_long_ext.cpp -I$(OBJ_DIR) $(OBJ_DIR)/eam.cubin: lal_eam.cu lal_precision.h lal_preprocessor.h $(CUDA) --cubin -DNV_KERNEL -o $@ lal_eam.cu diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile index 7ef1dfba0c..4a59595313 100644 --- a/lib/gpu/Opencl.makefile +++ b/lib/gpu/Opencl.makefile @@ -32,8 +32,8 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \ $(OBJ_DIR)/lal_coul_long.o $(OBJ_DIR)/lal_coul_long_ext.o \ $(OBJ_DIR)/lal_morse.o $(OBJ_DIR)/lal_morse_ext.o \ $(OBJ_DIR)/lal_charmm_long.o $(OBJ_DIR)/lal_charmm_long_ext.o \ - $(OBJ_DIR)/lal_cg_cmm.o $(OBJ_DIR)/lal_cg_cmm_ext.o \ - $(OBJ_DIR)/lal_cg_cmm_long.o $(OBJ_DIR)/lal_cg_cmm_long_ext.o \ + $(OBJ_DIR)/lal_lj_sdk.o $(OBJ_DIR)/lal_lj_sdk_ext.o \ + $(OBJ_DIR)/lal_lj_sdk_long.o $(OBJ_DIR)/lal_lj_sdk_long_ext.o \ $(OBJ_DIR)/lal_eam.o $(OBJ_DIR)/lal_eam_ext.o \ $(OBJ_DIR)/lal_eam_fs_ext.o $(OBJ_DIR)/lal_eam_alloy_ext.o \ $(OBJ_DIR)/lal_buck.o $(OBJ_DIR)/lal_buck_ext.o \ @@ -75,8 +75,8 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \ $(OBJ_DIR)/lj_coul_long_cl.h $(OBJ_DIR)/lj_dsf_cl.h \ $(OBJ_DIR)/lj_class2_long_cl.h \ $(OBJ_DIR)/coul_long_cl.h $(OBJ_DIR)/morse_cl.h \ - $(OBJ_DIR)/charmm_long_cl.h $(OBJ_DIR)/cg_cmm_cl.h \ - $(OBJ_DIR)/cg_cmm_long_cl.h $(OBJ_DIR)/neighbor_gpu_cl.h \ + $(OBJ_DIR)/charmm_long_cl.h $(OBJ_DIR)/lj_sdk_cl.h \ + $(OBJ_DIR)/lj_sdk_long_cl.h $(OBJ_DIR)/neighbor_gpu_cl.h \ $(OBJ_DIR)/eam_cl.h $(OBJ_DIR)/buck_cl.h \ $(OBJ_DIR)/buck_coul_cl.h $(OBJ_DIR)/buck_coul_long_cl.h \ $(OBJ_DIR)/table_cl.h $(OBJ_DIR)/yukawa_cl.h \ @@ -273,23 +273,23 @@ $(OBJ_DIR)/lal_lj_expand.o: $(ALL_H) lal_lj_expand.h lal_lj_expand.cpp $(OBJ_DI $(OBJ_DIR)/lal_lj_expand_ext.o: $(ALL_H) lal_lj_expand.h lal_lj_expand_ext.cpp lal_base_atomic.h $(OCL) -o $@ -c lal_lj_expand_ext.cpp -I$(OBJ_DIR) -$(OBJ_DIR)/cg_cmm_cl.h: lal_cg_cmm.cu $(PRE1_H) - $(BSH) ./geryon/file_to_cstr.sh cg_cmm $(PRE1_H) lal_cg_cmm.cu $(OBJ_DIR)/cg_cmm_cl.h; +$(OBJ_DIR)/lj_sdk_cl.h: lal_lj_sdk.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh lj_sdk $(PRE1_H) lal_lj_sdk.cu $(OBJ_DIR)/lj_sdk_cl.h; -$(OBJ_DIR)/lal_cg_cmm.o: $(ALL_H) lal_cg_cmm.h lal_cg_cmm.cpp $(OBJ_DIR)/cg_cmm_cl.h $(OBJ_DIR)/cg_cmm_cl.h $(OBJ_DIR)/lal_base_atomic.o - $(OCL) -o $@ -c lal_cg_cmm.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/lal_lj_sdk.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk.cpp $(OBJ_DIR)/lj_sdk_cl.h $(OBJ_DIR)/lj_sdk_cl.h $(OBJ_DIR)/lal_base_atomic.o + $(OCL) -o $@ -c lal_lj_sdk.cpp -I$(OBJ_DIR) -$(OBJ_DIR)/lal_cg_cmm_ext.o: $(ALL_H) lal_cg_cmm.h lal_cg_cmm_ext.cpp lal_base_atomic.h - $(OCL) -o $@ -c lal_cg_cmm_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/lal_lj_sdk_ext.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk_ext.cpp lal_base_atomic.h + $(OCL) -o $@ -c lal_lj_sdk_ext.cpp -I$(OBJ_DIR) -$(OBJ_DIR)/cg_cmm_long_cl.h: lal_cg_cmm_long.cu $(PRE1_H) - $(BSH) ./geryon/file_to_cstr.sh cg_cmm_long $(PRE1_H) lal_cg_cmm_long.cu $(OBJ_DIR)/cg_cmm_long_cl.h; +$(OBJ_DIR)/lj_sdk_long_cl.h: lal_lj_sdk_long.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh lj_sdk_long $(PRE1_H) lal_lj_sdk_long.cu $(OBJ_DIR)/lj_sdk_long_cl.h; -$(OBJ_DIR)/lal_cg_cmm_long.o: $(ALL_H) lal_cg_cmm_long.h lal_cg_cmm_long.cpp $(OBJ_DIR)/cg_cmm_long_cl.h $(OBJ_DIR)/cg_cmm_long_cl.h $(OBJ_DIR)/lal_base_atomic.o - $(OCL) -o $@ -c lal_cg_cmm_long.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/lal_lj_sdk_long.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long.cpp $(OBJ_DIR)/lj_sdk_long_cl.h $(OBJ_DIR)/lj_sdk_long_cl.h $(OBJ_DIR)/lal_base_atomic.o + $(OCL) -o $@ -c lal_lj_sdk_long.cpp -I$(OBJ_DIR) -$(OBJ_DIR)/lal_cg_cmm_long_ext.o: $(ALL_H) lal_cg_cmm_long.h lal_cg_cmm_long_ext.cpp lal_base_charge.h - $(OCL) -o $@ -c lal_cg_cmm_long_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/lal_lj_sdk_long_ext.o: $(ALL_H) lal_lj_sdk_long.h lal_lj_sdk_long_ext.cpp lal_base_charge.h + $(OCL) -o $@ -c lal_lj_sdk_long_ext.cpp -I$(OBJ_DIR) $(OBJ_DIR)/eam_cl.h: lal_eam.cu $(PRE1_H) $(BSH) ./geryon/file_to_cstr.sh eam $(PRE1_H) lal_eam.cu $(OBJ_DIR)/eam_cl.h; diff --git a/lib/gpu/lal_cg_cmm.cpp b/lib/gpu/lal_cg_cmm.cpp index d361e32b09..618555e38a 100644 --- a/lib/gpu/lal_cg_cmm.cpp +++ b/lib/gpu/lal_cg_cmm.cpp @@ -1,5 +1,5 @@ /*************************************************************************** - cg_cmm.cpp + lj_sdk.cpp ------------------- W. Michael Brown (ORNL) @@ -14,14 +14,14 @@ ***************************************************************************/ #if defined(USE_OPENCL) -#include "cg_cmm_cl.h" +#include "lj_sdk_cl.h" #elif defined(USE_CUDART) -const char *cg_cmm=0; +const char *lj_sdk=0; #else -#include "cg_cmm_cubin.h" +#include "lj_sdk_cubin.h" #endif -#include "lal_cg_cmm.h" +#include "lal_lj_sdk.h" #include using namespace LAMMPS_AL; #define CGCMMT CGCMM @@ -53,33 +53,33 @@ int CGCMMT::init(const int ntypes, double **host_cutsq, const double gpu_split, FILE *_screen) { int success; success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, - _screen,cg_cmm,"k_cg_cmm"); + _screen,lj_sdk,"k_lj_sdk"); if (success!=0) return success; // If atom type constants fit in shared memory use fast kernel - int cmm_types=ntypes; + int sdk_types=ntypes; shared_types=false; int max_shared_types=this->device->max_shared_types(); - if (cmm_types<=max_shared_types && this->_block_size>=max_shared_types) { - cmm_types=max_shared_types; + if (sdk_types<=max_shared_types && this->_block_size>=max_shared_types) { + sdk_types=max_shared_types; shared_types=true; } - _cmm_types=cmm_types; + _sdk_types=sdk_types; // Allocate a host write buffer for data initialization - UCL_H_Vec host_write(cmm_types*cmm_types*32,*(this->ucl_device), + UCL_H_Vec host_write(sdk_types*sdk_types*32,*(this->ucl_device), UCL_WRITE_ONLY); - for (int i=0; iucl_device),UCL_READ_ONLY); - this->atom->type_pack4(ntypes,cmm_types,lj1,host_write,host_cutsq, + lj1.alloc(sdk_types*sdk_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,sdk_types,lj1,host_write,host_cutsq, host_cg_type,host_lj1,host_lj2); - lj3.alloc(cmm_types*cmm_types,*(this->ucl_device),UCL_READ_ONLY); - this->atom->type_pack4(ntypes,cmm_types,lj3,host_write,host_lj3,host_lj4, + lj3.alloc(sdk_types*sdk_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,sdk_types,lj3,host_write,host_lj3,host_lj4, host_offset); UCL_H_Vec dview; @@ -143,7 +143,7 @@ void CGCMMT::loop(const bool _eflag, const bool _vflag) { } else { this->k_pair.set_size(GX,BX); this->k_pair.run(&this->atom->x, &lj1, &lj3, - &_cmm_types, &sp_lj, &this->nbor->dev_nbor, + &_sdk_types, &sp_lj, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom); diff --git a/lib/gpu/lal_cg_cmm.cu b/lib/gpu/lal_cg_cmm.cu index 70d2ab6092..01b2cdd18d 100644 --- a/lib/gpu/lal_cg_cmm.cu +++ b/lib/gpu/lal_cg_cmm.cu @@ -1,5 +1,5 @@ // ************************************************************************** -// cg_cmm.cu +// lj_sdk.cu // ------------------- // W. Michael Brown (ORNL) // @@ -24,7 +24,7 @@ texture pos_tex; #define pos_tex x_ #endif -__kernel void k_cg_cmm(const __global numtyp4 *restrict x_, +__kernel void k_lj_sdk(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1, const __global numtyp4 *restrict lj3, const int lj_types, @@ -116,7 +116,7 @@ __kernel void k_cg_cmm(const __global numtyp4 *restrict x_, } // if ii } -__kernel void k_cg_cmm_fast(const __global numtyp4 *restrict x_, +__kernel void k_lj_sdk_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1_in, const __global numtyp4 *restrict lj3_in, const __global numtyp *restrict sp_lj_in, diff --git a/lib/gpu/lal_cg_cmm.h b/lib/gpu/lal_cg_cmm.h index b7895b5898..ac2b9aafe3 100644 --- a/lib/gpu/lal_cg_cmm.h +++ b/lib/gpu/lal_cg_cmm.h @@ -1,5 +1,5 @@ /*************************************************************************** - cg_cmm.h + lj_sdk.h ------------------- W. Michael Brown (ORNL) @@ -67,7 +67,7 @@ class CGCMM : public BaseAtomic { bool shared_types; /// Number of atom types - int _cmm_types; + int _sdk_types; private: bool _allocated; diff --git a/lib/gpu/lal_cg_cmm_ext.cpp b/lib/gpu/lal_cg_cmm_ext.cpp index b6fc110b15..386106161e 100644 --- a/lib/gpu/lal_cg_cmm_ext.cpp +++ b/lib/gpu/lal_cg_cmm_ext.cpp @@ -1,5 +1,5 @@ /*************************************************************************** - cg_cmm.h + lj_sdk.h ------------------- W. Michael Brown (ORNL) @@ -17,7 +17,7 @@ #include #include -#include "lal_cg_cmm.h" +#include "lal_lj_sdk.h" using namespace std; using namespace LAMMPS_AL; @@ -27,7 +27,7 @@ static CGCMM CMMMF; // --------------------------------------------------------------------------- // Allocate memory on host and device and copy constants to device // --------------------------------------------------------------------------- -int cmm_gpu_init(const int ntypes, double **cutsq, int **cg_types, +int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int inum, const int nall, const int max_nbors, @@ -89,11 +89,11 @@ int cmm_gpu_init(const int ntypes, double **cutsq, int **cg_types, return init_ok; } -void cmm_gpu_clear() { +void sdk_gpu_clear() { CMMMF.clear(); } -int** cmm_gpu_compute_n(const int ago, const int inum_full, +int** sdk_gpu_compute_n(const int ago, const int inum_full, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special, const bool eflag, const bool vflag, @@ -105,7 +105,7 @@ int** cmm_gpu_compute_n(const int ago, const int inum_full, vatom, host_start, ilist, jnum, cpu_time, success); } -void cmm_gpu_compute(const int ago, const int inum_full, const int nall, +void sdk_gpu_compute(const int ago, const int inum_full, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, @@ -114,7 +114,7 @@ void cmm_gpu_compute(const int ago, const int inum_full, const int nall, firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success); } -double cmm_gpu_bytes() { +double sdk_gpu_bytes() { return CMMMF.host_memory_usage(); } diff --git a/lib/gpu/lal_cg_cmm_long.cpp b/lib/gpu/lal_cg_cmm_long.cpp index 14b5b7622c..46caf6bd36 100644 --- a/lib/gpu/lal_cg_cmm_long.cpp +++ b/lib/gpu/lal_cg_cmm_long.cpp @@ -1,5 +1,5 @@ /*************************************************************************** - cg_cmm_long.cpp + lj_sdk_long.cpp ------------------- W. Michael Brown (ORNL) @@ -14,14 +14,14 @@ ***************************************************************************/ #if defined(USE_OPENCL) -#include "cg_cmm_long_cl.h" +#include "lj_sdk_long_cl.h" #elif defined(USE_CUDART) -const char *cg_cmm_long=0; +const char *lj_sdk_long=0; #else -#include "cg_cmm_long_cubin.h" +#include "lj_sdk_long_cubin.h" #endif -#include "lal_cg_cmm_long.h" +#include "lal_lj_sdk_long.h" #include using namespace LAMMPS_AL; #define CGCMMLongT CGCMMLong @@ -58,7 +58,7 @@ int CGCMMLongT::init(const int ntypes, double **host_cutsq, const double g_ewald) { int success; success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, - _screen,cg_cmm_long,"k_cg_cmm_long"); + _screen,lj_sdk_long,"k_lj_sdk_long"); if (success!=0) return success; diff --git a/lib/gpu/lal_cg_cmm_long.cu b/lib/gpu/lal_cg_cmm_long.cu index f6942d1809..5ff64b2254 100644 --- a/lib/gpu/lal_cg_cmm_long.cu +++ b/lib/gpu/lal_cg_cmm_long.cu @@ -1,5 +1,5 @@ // ************************************************************************** -// cg_cmm_long.cu +// lj_sdk_long.cu // ------------------- // W. Michael Brown (ORNL) // @@ -29,7 +29,7 @@ texture q_tex; #define q_tex q_ #endif -__kernel void k_cg_cmm_long(const __global numtyp4 *restrict x_, +__kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1, const __global numtyp4 *restrict lj3, const int lj_types, @@ -154,7 +154,7 @@ __kernel void k_cg_cmm_long(const __global numtyp4 *restrict x_, } // if ii } -__kernel void k_cg_cmm_long_fast(const __global numtyp4 *restrict x_, +__kernel void k_lj_sdk_long_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1_in, const __global numtyp4 *restrict lj3_in, const __global numtyp *restrict sp_lj_in, diff --git a/lib/gpu/lal_cg_cmm_long.h b/lib/gpu/lal_cg_cmm_long.h index aa0cbfbaf0..f56687cd7d 100644 --- a/lib/gpu/lal_cg_cmm_long.h +++ b/lib/gpu/lal_cg_cmm_long.h @@ -1,5 +1,5 @@ /*************************************************************************** - cg_cmm_long.h + lj_sdk_long.h ------------------- W. Michael Brown (ORNL) diff --git a/lib/gpu/lal_cg_cmm_long_ext.cpp b/lib/gpu/lal_cg_cmm_long_ext.cpp index ee0a0269e5..08390d3eeb 100644 --- a/lib/gpu/lal_cg_cmm_long_ext.cpp +++ b/lib/gpu/lal_cg_cmm_long_ext.cpp @@ -1,5 +1,5 @@ /*************************************************************************** - cg_cmm_long.h + lj_sdk_long.h ------------------- W. Michael Brown (ORNL) @@ -17,7 +17,7 @@ #include #include -#include "lal_cg_cmm_long.h" +#include "lal_lj_sdk_long.h" using namespace std; using namespace LAMMPS_AL; @@ -27,7 +27,7 @@ static CGCMMLong CMMLMF; // --------------------------------------------------------------------------- // Allocate memory on host and device and copy constants to device // --------------------------------------------------------------------------- -int cmml_gpu_init(const int ntypes, double **cutsq, int **cg_type, +int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int inum, const int nall, const int max_nbors, @@ -93,11 +93,11 @@ int cmml_gpu_init(const int ntypes, double **cutsq, int **cg_type, return init_ok; } -void cmml_gpu_clear() { +void sdkl_gpu_clear() { CMMLMF.clear(); } -int** cmml_gpu_compute_n(const int ago, const int inum_full, +int** sdkl_gpu_compute_n(const int ago, const int inum_full, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special, const bool eflag, const bool vflag, @@ -111,7 +111,7 @@ int** cmml_gpu_compute_n(const int ago, const int inum_full, host_q,boxlo,prd); } -void cmml_gpu_compute(const int ago, const int inum_full, const int nall, +void sdkl_gpu_compute(const int ago, const int inum_full, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, @@ -122,7 +122,7 @@ void cmml_gpu_compute(const int ago, const int inum_full, const int nall, host_q,nlocal,boxlo,prd); } -double cmml_gpu_bytes() { +double sdkl_gpu_bytes() { return CMMLMF.host_memory_usage(); } diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index 0b8d0f3b31..77c0dc0660 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -48,7 +48,7 @@ using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition -int cmml_gpu_init(const int ntypes, double **cutsq, int **lj_type, +int sdkl_gpu_init(const int ntypes, double **cutsq, int **lj_type, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int nlocal, const int nall, const int max_nbors, @@ -56,8 +56,8 @@ int cmml_gpu_init(const int ntypes, double **cutsq, int **lj_type, FILE *screen, double **host_cut_ljsq, double host_cut_coulsq, double *host_special_coul, const double qqrd2e, const double g_ewald); -void cmml_gpu_clear(); -int ** cmml_gpu_compute_n(const int ago, const int inum, const int nall, +void sdkl_gpu_clear(); +int ** sdkl_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special, const bool eflag, const bool vflag, @@ -65,13 +65,13 @@ int ** cmml_gpu_compute_n(const int ago, const int inum, const int nall, int **ilist, int **jnum, const double cpu_time, bool &success, double *host_q, double *boxlo, double *prd); -void cmml_gpu_compute(const int ago, const int inum, const int nall, +void sdkl_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, const double cpu_time, bool &success, double *host_q, const int nlocal, double *boxlo, double *prd); -double cmml_gpu_bytes(); +double sdkl_gpu_bytes(); #include "lj_sdk_common.h" @@ -95,7 +95,7 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) : PairLJSDKCoulLongGPU::~PairLJSDKCoulLongGPU() { - cmml_gpu_clear(); + sdkl_gpu_clear(); } /* ---------------------------------------------------------------------- */ @@ -112,7 +112,7 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag) int *ilist, *numneigh, **firstneigh; if (gpu_mode != GPU_FORCE) { inum = atom->nlocal; - firstneigh = cmml_gpu_compute_n(neighbor->ago, inum, nall, atom->x, + firstneigh = sdkl_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, domain->sublo, domain->subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom, @@ -124,7 +124,7 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag) ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - cmml_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, + sdkl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->q, atom->nlocal, domain->boxlo, domain->prd); @@ -185,7 +185,7 @@ void PairLJSDKCoulLongGPU::init_style() int maxspecial=0; if (atom->molecular) maxspecial=atom->maxspecial; - int success = cmml_gpu_init(atom->ntypes+1, cutsq, lj_type, lj1, lj2, lj3, + int success = sdkl_gpu_init(atom->ntypes+1, cutsq, lj_type, lj1, lj2, lj3, lj4, offset, force->special_lj, atom->nlocal, atom->nlocal+atom->nghost, 300, maxspecial, cell_size, gpu_mode, screen, cut_ljsq, @@ -205,7 +205,7 @@ void PairLJSDKCoulLongGPU::init_style() double PairLJSDKCoulLongGPU::memory_usage() { double bytes = Pair::memory_usage(); - return bytes + cmml_gpu_bytes(); + return bytes + sdkl_gpu_bytes(); } /* ---------------------------------------------------------------------- */ diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index e7e9b690f3..67103181d5 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -39,26 +39,26 @@ using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition -int cmm_gpu_init(const int ntypes, double **cutsq, int **cg_types, +int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen); -void cmm_gpu_clear(); -int ** cmm_gpu_compute_n(const int ago, const int inum, const int nall, +void sdk_gpu_clear(); +int ** sdk_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, int **ilist, int **jnum, const double cpu_time, bool &success); -void cmm_gpu_compute(const int ago, const int inum, const int nall, +void sdk_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, const double cpu_time, bool &success); -double cmm_gpu_bytes(); +double sdk_gpu_bytes(); #include "lj_sdk_common.h" @@ -80,7 +80,7 @@ PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE) PairLJSDKGPU::~PairLJSDKGPU() { - cmm_gpu_clear(); + sdk_gpu_clear(); } /* ---------------------------------------------------------------------- */ @@ -97,7 +97,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag) int *ilist, *numneigh, **firstneigh; if (gpu_mode != GPU_FORCE) { inum = atom->nlocal; - firstneigh = cmm_gpu_compute_n(neighbor->ago, inum, nall, atom->x, + firstneigh = sdk_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, domain->sublo, domain->subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom, @@ -108,7 +108,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag) ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - cmm_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, + sdk_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success); } @@ -154,7 +154,7 @@ void PairLJSDKGPU::init_style() int maxspecial=0; if (atom->molecular) maxspecial=atom->maxspecial; - int success = cmm_gpu_init(atom->ntypes+1,cutsq,lj_type,lj1,lj2,lj3,lj4, + int success = sdk_gpu_init(atom->ntypes+1,cutsq,lj_type,lj1,lj2,lj3,lj4, offset, force->special_lj, atom->nlocal, atom->nlocal+atom->nghost, 300, maxspecial, cell_size, gpu_mode, screen); @@ -172,7 +172,7 @@ void PairLJSDKGPU::init_style() double PairLJSDKGPU::memory_usage() { double bytes = Pair::memory_usage(); - return bytes + cmm_gpu_bytes(); + return bytes + sdk_gpu_bytes(); } /* ---------------------------------------------------------------------- */ From b8cb80b219b802d9713e69ea13699c8771be25e0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 26 Apr 2017 19:46:10 -0400 Subject: [PATCH 7/7] rename files in GPU library from cg_cmm to lj_sdk --- lib/gpu/{lal_cg_cmm.cpp => lal_lj_sdk.cpp} | 0 lib/gpu/{lal_cg_cmm.cu => lal_lj_sdk.cu} | 0 lib/gpu/{lal_cg_cmm.h => lal_lj_sdk.h} | 0 lib/gpu/{lal_cg_cmm_ext.cpp => lal_lj_sdk_ext.cpp} | 0 lib/gpu/{lal_cg_cmm_long.cpp => lal_lj_sdk_long.cpp} | 0 lib/gpu/{lal_cg_cmm_long.cu => lal_lj_sdk_long.cu} | 0 lib/gpu/{lal_cg_cmm_long.h => lal_lj_sdk_long.h} | 0 lib/gpu/{lal_cg_cmm_long_ext.cpp => lal_lj_sdk_long_ext.cpp} | 0 8 files changed, 0 insertions(+), 0 deletions(-) rename lib/gpu/{lal_cg_cmm.cpp => lal_lj_sdk.cpp} (100%) rename lib/gpu/{lal_cg_cmm.cu => lal_lj_sdk.cu} (100%) rename lib/gpu/{lal_cg_cmm.h => lal_lj_sdk.h} (100%) rename lib/gpu/{lal_cg_cmm_ext.cpp => lal_lj_sdk_ext.cpp} (100%) rename lib/gpu/{lal_cg_cmm_long.cpp => lal_lj_sdk_long.cpp} (100%) rename lib/gpu/{lal_cg_cmm_long.cu => lal_lj_sdk_long.cu} (100%) rename lib/gpu/{lal_cg_cmm_long.h => lal_lj_sdk_long.h} (100%) rename lib/gpu/{lal_cg_cmm_long_ext.cpp => lal_lj_sdk_long_ext.cpp} (100%) diff --git a/lib/gpu/lal_cg_cmm.cpp b/lib/gpu/lal_lj_sdk.cpp similarity index 100% rename from lib/gpu/lal_cg_cmm.cpp rename to lib/gpu/lal_lj_sdk.cpp diff --git a/lib/gpu/lal_cg_cmm.cu b/lib/gpu/lal_lj_sdk.cu similarity index 100% rename from lib/gpu/lal_cg_cmm.cu rename to lib/gpu/lal_lj_sdk.cu diff --git a/lib/gpu/lal_cg_cmm.h b/lib/gpu/lal_lj_sdk.h similarity index 100% rename from lib/gpu/lal_cg_cmm.h rename to lib/gpu/lal_lj_sdk.h diff --git a/lib/gpu/lal_cg_cmm_ext.cpp b/lib/gpu/lal_lj_sdk_ext.cpp similarity index 100% rename from lib/gpu/lal_cg_cmm_ext.cpp rename to lib/gpu/lal_lj_sdk_ext.cpp diff --git a/lib/gpu/lal_cg_cmm_long.cpp b/lib/gpu/lal_lj_sdk_long.cpp similarity index 100% rename from lib/gpu/lal_cg_cmm_long.cpp rename to lib/gpu/lal_lj_sdk_long.cpp diff --git a/lib/gpu/lal_cg_cmm_long.cu b/lib/gpu/lal_lj_sdk_long.cu similarity index 100% rename from lib/gpu/lal_cg_cmm_long.cu rename to lib/gpu/lal_lj_sdk_long.cu diff --git a/lib/gpu/lal_cg_cmm_long.h b/lib/gpu/lal_lj_sdk_long.h similarity index 100% rename from lib/gpu/lal_cg_cmm_long.h rename to lib/gpu/lal_lj_sdk_long.h diff --git a/lib/gpu/lal_cg_cmm_long_ext.cpp b/lib/gpu/lal_lj_sdk_long_ext.cpp similarity index 100% rename from lib/gpu/lal_cg_cmm_long_ext.cpp rename to lib/gpu/lal_lj_sdk_long_ext.cpp