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Merge pull request #464 from akohlmey/rename-cg-cmm-to-cgsdk

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Rename USER-CG-CMM package to USER-CGSDK
This commit is contained in:
sjplimp
2017-05-03 08:37:20 -06:00
committed by GitHub
parent 2f32fb7f8b b8cb80b219
commit f5cf1f1314
46 changed files with 133 additions and 149 deletions
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2
doc/src/Section_intro.txt
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@ -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 code would not be as general-purpose as it is without their expertise
and efforts. 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 Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU package Mike Brown (ORNL), brownw at ornl.gov, GPU package
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential

32
doc/src/Section_packages.txt
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@ -1139,8 +1139,8 @@ The current list of user-contributed packages is as follows:
Package, Description, Author(s), Doc page, Example, Pic/movie, Library 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-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-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-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-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-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, -, - "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) :tb(ea=c)
:link(atc,http://lammps.sandia.gov/pictures.html#atc) :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(eff,http://lammps.sandia.gov/movies.html#eff)
:link(manifold,http://lammps.sandia.gov/movies.html#manifold) :link(manifold,http://lammps.sandia.gov/movies.html#manifold)
:link(sph,http://lammps.sandia.gov/movies.html#sph) :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 :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 Contents: CGSDK stands for Shinoda-DeVane-Klein (SDK) coarse-grained
implements several pair styles and an angle style using the coarse molecular dynamics force field. This package implements several pair
grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 styles and an angle style using the coarse grained parametrization of
(2007) (SDK), with extensions to simulate ionic liquids, electrolytes, Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) (SDK), with extensions
lipids and charged amino acids. See src/USER-CG-CMM/README for more to simulate ionic liquids, electrolytes, lipids and charged amino acids.
details. 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, "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 Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact
him directly if you have questions. 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 colvars"_fix_colvars.html, examples/USER/colvars
Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the
fix. The COLVARS library itself is written and maintained by Giacomo interface that integrates colvars into LAMMPS. The COLVARS library
Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome itself is written and maintained by Giacomo Fiorin (ICMS, Temple
Henin (LISM, CNRS, Marseille, France). Contact them directly if you University, Philadelphia, PA, USA) and Jerome Henin (LISM, CNRS,
have questions. 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 :line

2
doc/src/angle_sdk.txt
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@ -46,7 +46,7 @@ from the pair_style.
[Restrictions:] [Restrictions:]
This angle style can only be used if LAMMPS was built with the 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. LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:] [Related commands:]

2
doc/src/pair_sdk.txt
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@ -134,7 +134,7 @@ respa"_run_style.html command.
[Restrictions:] [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 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 built (which is enabled by default). They are only enabled if LAMMPS
was built with that package. See the "Making was built with that package. See the "Making

2
examples/USER/cg-cmm/README → examples/USER/cgsdk/README
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@ -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 Each of these sub-directories contains a sample problem for the SDK
coarse grained MD potentials that you can run with LAMMPS. coarse grained MD potentials that you can run with LAMMPS.

0
examples/USER/cg-cmm/peg-verlet/data.pegc12e8.gz → examples/USER/cgsdk/peg-verlet/data.pegc12e8.gz
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0
examples/USER/cg-cmm/peg-verlet/in.pegc12e8 → examples/USER/cgsdk/peg-verlet/in.pegc12e8
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0
examples/USER/cg-cmm/peg-verlet/in.pegc12e8-angle → examples/USER/cgsdk/peg-verlet/in.pegc12e8-angle
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0
examples/USER/cg-cmm/peg-verlet/log.pegc12e8 → examples/USER/cgsdk/peg-verlet/log.pegc12e8
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0
examples/USER/cg-cmm/peg-verlet/log.pegc12e8-angle → examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle
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0
examples/USER/cg-cmm/sds-monolayer/data.sds.gz → examples/USER/cgsdk/sds-monolayer/data.sds.gz
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0
examples/USER/cg-cmm/sds-monolayer/in.sds-hybrid → examples/USER/cgsdk/sds-monolayer/in.sds-hybrid
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0
examples/USER/cg-cmm/sds-monolayer/in.sds-regular → examples/USER/cgsdk/sds-monolayer/in.sds-regular
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0
examples/USER/cg-cmm/sds-monolayer/log.sds-hybrid → examples/USER/cgsdk/sds-monolayer/log.sds-hybrid
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0
examples/USER/cg-cmm/sds-monolayer/log.sds-regular → examples/USER/cgsdk/sds-monolayer/log.sds-regular
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40
lib/gpu/Nvidia.makefile
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@ -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_coul_long.o $(OBJ_DIR)/lal_coul_long_ext.o \
$(OBJ_DIR)/lal_morse.o $(OBJ_DIR)/lal_morse_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_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_lj_sdk.o $(OBJ_DIR)/lal_lj_sdk_ext.o \
$(OBJ_DIR)/lal_cg_cmm_long.o $(OBJ_DIR)/lal_cg_cmm_long_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.o $(OBJ_DIR)/lal_eam_ext.o \
$(OBJ_DIR)/lal_eam_fs_ext.o $(OBJ_DIR)/lal_eam_alloy_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 \ $(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)/coul_long.cubin $(OBJ_DIR)/coul_long_cubin.h \
$(OBJ_DIR)/morse.cubin $(OBJ_DIR)/morse_cubin.h \ $(OBJ_DIR)/morse.cubin $(OBJ_DIR)/morse_cubin.h \
$(OBJ_DIR)/charmm_long.cubin $(OBJ_DIR)/charmm_long_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)/lj_sdk.cubin $(OBJ_DIR)/lj_sdk_cubin.h \
$(OBJ_DIR)/cg_cmm_long.cubin $(OBJ_DIR)/cg_cmm_long_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)/eam.cubin $(OBJ_DIR)/eam_cubin.h \
$(OBJ_DIR)/buck.cubin $(OBJ_DIR)/buck_cubin.h \ $(OBJ_DIR)/buck.cubin $(OBJ_DIR)/buck_cubin.h \
$(OBJ_DIR)/buck_coul_long.cubin $(OBJ_DIR)/buck_coul_long_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 $(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) $(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 $(OBJ_DIR)/lj_sdk.cubin: lal_lj_sdk.cu lal_precision.h lal_preprocessor.h
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_cg_cmm.cu $(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 $(OBJ_DIR)/lj_sdk_cubin.h: $(OBJ_DIR)/lj_sdk.cubin $(OBJ_DIR)/lj_sdk.cubin
$(BIN2C) -c -n cg_cmm $(OBJ_DIR)/cg_cmm.cubin > $(OBJ_DIR)/cg_cmm_cubin.h $(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 $(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 $@ -c lal_cg_cmm.cpp -I$(OBJ_DIR) $(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 $(OBJ_DIR)/lal_lj_sdk_ext.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk_ext.cpp lal_base_atomic.h
$(CUDR) -o $@ -c lal_cg_cmm_ext.cpp -I$(OBJ_DIR) $(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 $(OBJ_DIR)/lj_sdk_long.cubin: lal_lj_sdk_long.cu lal_precision.h lal_preprocessor.h
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_cg_cmm_long.cu $(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 $(OBJ_DIR)/lj_sdk_long_cubin.h: $(OBJ_DIR)/lj_sdk_long.cubin $(OBJ_DIR)/lj_sdk_long.cubin
$(BIN2C) -c -n cg_cmm_long $(OBJ_DIR)/cg_cmm_long.cubin > $(OBJ_DIR)/cg_cmm_long_cubin.h $(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 $(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 $@ -c lal_cg_cmm_long.cpp -I$(OBJ_DIR) $(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 $(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 $@ -c lal_cg_cmm_long_ext.cpp -I$(OBJ_DIR) $(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 $(OBJ_DIR)/eam.cubin: lal_eam.cu lal_precision.h lal_preprocessor.h
$(CUDA) --cubin -DNV_KERNEL -o $@ lal_eam.cu $(CUDA) --cubin -DNV_KERNEL -o $@ lal_eam.cu

32
lib/gpu/Opencl.makefile
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@ -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_coul_long.o $(OBJ_DIR)/lal_coul_long_ext.o \
$(OBJ_DIR)/lal_morse.o $(OBJ_DIR)/lal_morse_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_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_lj_sdk.o $(OBJ_DIR)/lal_lj_sdk_ext.o \
$(OBJ_DIR)/lal_cg_cmm_long.o $(OBJ_DIR)/lal_cg_cmm_long_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.o $(OBJ_DIR)/lal_eam_ext.o \
$(OBJ_DIR)/lal_eam_fs_ext.o $(OBJ_DIR)/lal_eam_alloy_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 \ $(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_coul_long_cl.h $(OBJ_DIR)/lj_dsf_cl.h \
$(OBJ_DIR)/lj_class2_long_cl.h \ $(OBJ_DIR)/lj_class2_long_cl.h \
$(OBJ_DIR)/coul_long_cl.h $(OBJ_DIR)/morse_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)/charmm_long_cl.h $(OBJ_DIR)/lj_sdk_cl.h \
$(OBJ_DIR)/cg_cmm_long_cl.h $(OBJ_DIR)/neighbor_gpu_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)/eam_cl.h $(OBJ_DIR)/buck_cl.h \
$(OBJ_DIR)/buck_coul_cl.h $(OBJ_DIR)/buck_coul_long_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 \ $(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 $(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) $(OCL) -o $@ -c lal_lj_expand_ext.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/cg_cmm_cl.h: lal_cg_cmm.cu $(PRE1_H) $(OBJ_DIR)/lj_sdk_cl.h: lal_lj_sdk.cu $(PRE1_H)
$(BSH) ./geryon/file_to_cstr.sh cg_cmm $(PRE1_H) lal_cg_cmm.cu $(OBJ_DIR)/cg_cmm_cl.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 $(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 $@ -c lal_cg_cmm.cpp -I$(OBJ_DIR) $(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 $(OBJ_DIR)/lal_lj_sdk_ext.o: $(ALL_H) lal_lj_sdk.h lal_lj_sdk_ext.cpp lal_base_atomic.h
$(OCL) -o $@ -c lal_cg_cmm_ext.cpp -I$(OBJ_DIR) $(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) $(OBJ_DIR)/lj_sdk_long_cl.h: lal_lj_sdk_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; $(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 $(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 $@ -c lal_cg_cmm_long.cpp -I$(OBJ_DIR) $(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 $(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 $@ -c lal_cg_cmm_long_ext.cpp -I$(OBJ_DIR) $(OCL) -o $@ -c lal_lj_sdk_long_ext.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/eam_cl.h: lal_eam.cu $(PRE1_H) $(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; $(BSH) ./geryon/file_to_cstr.sh eam $(PRE1_H) lal_eam.cu $(OBJ_DIR)/eam_cl.h;

34
lib/gpu/lal_cg_cmm.cpp → lib/gpu/lal_lj_sdk.cpp
View File

@ -1,5 +1,5 @@
/*************************************************************************** /***************************************************************************
cg_cmm.cpp lj_sdk.cpp
------------------- -------------------
W. Michael Brown (ORNL) W. Michael Brown (ORNL)
@ -14,14 +14,14 @@
***************************************************************************/ ***************************************************************************/
#if defined(USE_OPENCL) #if defined(USE_OPENCL)
#include "cg_cmm_cl.h" #include "lj_sdk_cl.h"
#elif defined(USE_CUDART) #elif defined(USE_CUDART)
const char *cg_cmm=0; const char *lj_sdk=0;
#else #else
#include "cg_cmm_cubin.h" #include "lj_sdk_cubin.h"
#endif #endif
#include "lal_cg_cmm.h" #include "lal_lj_sdk.h"
#include <cassert> #include <cassert>
using namespace LAMMPS_AL; using namespace LAMMPS_AL;
#define CGCMMT CGCMM<numtyp, acctyp> #define CGCMMT CGCMM<numtyp, acctyp>
@ -53,33 +53,33 @@ int CGCMMT::init(const int ntypes, double **host_cutsq,
const double gpu_split, FILE *_screen) { const double gpu_split, FILE *_screen) {
int success; int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, 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) if (success!=0)
return success; return success;
// If atom type constants fit in shared memory use fast kernel // If atom type constants fit in shared memory use fast kernel
int cmm_types=ntypes; int sdk_types=ntypes;
shared_types=false; shared_types=false;
int max_shared_types=this->device->max_shared_types(); int max_shared_types=this->device->max_shared_types();
if (cmm_types<=max_shared_types && this->_block_size>=max_shared_types) { if (sdk_types<=max_shared_types && this->_block_size>=max_shared_types) {
cmm_types=max_shared_types; sdk_types=max_shared_types;
shared_types=true; shared_types=true;
} }
_cmm_types=cmm_types; _sdk_types=sdk_types;
// Allocate a host write buffer for data initialization // Allocate a host write buffer for data initialization
UCL_H_Vec<numtyp> host_write(cmm_types*cmm_types*32,*(this->ucl_device), UCL_H_Vec<numtyp> host_write(sdk_types*sdk_types*32,*(this->ucl_device),
UCL_WRITE_ONLY); UCL_WRITE_ONLY);
for (int i=0; i<cmm_types*cmm_types; i++) for (int i=0; i<sdk_types*sdk_types; i++)
host_write[i]=0.0; host_write[i]=0.0;
lj1.alloc(cmm_types*cmm_types,*(this->ucl_device),UCL_READ_ONLY); lj1.alloc(sdk_types*sdk_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,cmm_types,lj1,host_write,host_cutsq, this->atom->type_pack4(ntypes,sdk_types,lj1,host_write,host_cutsq,
host_cg_type,host_lj1,host_lj2); host_cg_type,host_lj1,host_lj2);
lj3.alloc(cmm_types*cmm_types,*(this->ucl_device),UCL_READ_ONLY); lj3.alloc(sdk_types*sdk_types,*(this->ucl_device),UCL_READ_ONLY);
this->atom->type_pack4(ntypes,cmm_types,lj3,host_write,host_lj3,host_lj4, this->atom->type_pack4(ntypes,sdk_types,lj3,host_write,host_lj3,host_lj4,
host_offset); host_offset);
UCL_H_Vec<double> dview; UCL_H_Vec<double> dview;
@ -143,7 +143,7 @@ void CGCMMT::loop(const bool _eflag, const bool _vflag) {
} else { } else {
this->k_pair.set_size(GX,BX); this->k_pair.set_size(GX,BX);
this->k_pair.run(&this->atom->x, &lj1, &lj3, 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->_nbor_data->begin(), &this->ans->force,
&this->ans->engv, &eflag, &vflag, &ainum, &this->ans->engv, &eflag, &vflag, &ainum,
&nbor_pitch, &this->_threads_per_atom); &nbor_pitch, &this->_threads_per_atom);

6
lib/gpu/lal_cg_cmm.cu → lib/gpu/lal_lj_sdk.cu
View File

@ -1,5 +1,5 @@
// ************************************************************************** // **************************************************************************
// cg_cmm.cu // lj_sdk.cu
// ------------------- // -------------------
// W. Michael Brown (ORNL) // W. Michael Brown (ORNL)
// //
@ -24,7 +24,7 @@ texture<int4,1> pos_tex;
#define pos_tex x_ #define pos_tex x_
#endif #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 lj1,
const __global numtyp4 *restrict lj3, const __global numtyp4 *restrict lj3,
const int lj_types, const int lj_types,
@ -116,7 +116,7 @@ __kernel void k_cg_cmm(const __global numtyp4 *restrict x_,
} // if ii } // 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 lj1_in,
const __global numtyp4 *restrict lj3_in, const __global numtyp4 *restrict lj3_in,
const __global numtyp *restrict sp_lj_in, const __global numtyp *restrict sp_lj_in,

4
lib/gpu/lal_cg_cmm.h → lib/gpu/lal_lj_sdk.h
View File

@ -1,5 +1,5 @@
/*************************************************************************** /***************************************************************************
cg_cmm.h lj_sdk.h
------------------- -------------------
W. Michael Brown (ORNL) W. Michael Brown (ORNL)
@ -67,7 +67,7 @@ class CGCMM : public BaseAtomic<numtyp, acctyp> {
bool shared_types; bool shared_types;
/// Number of atom types /// Number of atom types
int _cmm_types; int _sdk_types;
private: private:
bool _allocated; bool _allocated;

14
lib/gpu/lal_cg_cmm_ext.cpp → lib/gpu/lal_lj_sdk_ext.cpp
View File

@ -1,5 +1,5 @@
/*************************************************************************** /***************************************************************************
cg_cmm.h lj_sdk.h
------------------- -------------------
W. Michael Brown (ORNL) W. Michael Brown (ORNL)
@ -17,7 +17,7 @@
#include <cassert> #include <cassert>
#include <math.h> #include <math.h>
#include "lal_cg_cmm.h" #include "lal_lj_sdk.h"
using namespace std; using namespace std;
using namespace LAMMPS_AL; using namespace LAMMPS_AL;
@ -27,7 +27,7 @@ static CGCMM<PRECISION,ACC_PRECISION> CMMMF;
// --------------------------------------------------------------------------- // ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device // 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_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj, double **host_lj4, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors, 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; return init_ok;
} }
void cmm_gpu_clear() { void sdk_gpu_clear() {
CMMMF.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, const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial, double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag, 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); 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, double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag, int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start, 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); firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success);
} }
double cmm_gpu_bytes() { double sdk_gpu_bytes() {
return CMMMF.host_memory_usage(); return CMMMF.host_memory_usage();
} }

12
lib/gpu/lal_cg_cmm_long.cpp → lib/gpu/lal_lj_sdk_long.cpp
View File

@ -1,5 +1,5 @@
/*************************************************************************** /***************************************************************************
cg_cmm_long.cpp lj_sdk_long.cpp
------------------- -------------------
W. Michael Brown (ORNL) W. Michael Brown (ORNL)
@ -14,14 +14,14 @@
***************************************************************************/ ***************************************************************************/
#if defined(USE_OPENCL) #if defined(USE_OPENCL)
#include "cg_cmm_long_cl.h" #include "lj_sdk_long_cl.h"
#elif defined(USE_CUDART) #elif defined(USE_CUDART)
const char *cg_cmm_long=0; const char *lj_sdk_long=0;
#else #else
#include "cg_cmm_long_cubin.h" #include "lj_sdk_long_cubin.h"
#endif #endif
#include "lal_cg_cmm_long.h" #include "lal_lj_sdk_long.h"
#include <cassert> #include <cassert>
using namespace LAMMPS_AL; using namespace LAMMPS_AL;
#define CGCMMLongT CGCMMLong<numtyp, acctyp> #define CGCMMLongT CGCMMLong<numtyp, acctyp>
@ -58,7 +58,7 @@ int CGCMMLongT::init(const int ntypes, double **host_cutsq,
const double g_ewald) { const double g_ewald) {
int success; int success;
success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, 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) if (success!=0)
return success; return success;

6
lib/gpu/lal_cg_cmm_long.cu → lib/gpu/lal_lj_sdk_long.cu
View File

@ -1,5 +1,5 @@
// ************************************************************************** // **************************************************************************
// cg_cmm_long.cu // lj_sdk_long.cu
// ------------------- // -------------------
// W. Michael Brown (ORNL) // W. Michael Brown (ORNL)
// //
@ -29,7 +29,7 @@ texture<int2> q_tex;
#define q_tex q_ #define q_tex q_
#endif #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 lj1,
const __global numtyp4 *restrict lj3, const __global numtyp4 *restrict lj3,
const int lj_types, const int lj_types,
@ -154,7 +154,7 @@ __kernel void k_cg_cmm_long(const __global numtyp4 *restrict x_,
} // if ii } // 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 lj1_in,
const __global numtyp4 *restrict lj3_in, const __global numtyp4 *restrict lj3_in,
const __global numtyp *restrict sp_lj_in, const __global numtyp *restrict sp_lj_in,

2
lib/gpu/lal_cg_cmm_long.h → lib/gpu/lal_lj_sdk_long.h
View File

@ -1,5 +1,5 @@
/*************************************************************************** /***************************************************************************
cg_cmm_long.h lj_sdk_long.h
------------------- -------------------
W. Michael Brown (ORNL) W. Michael Brown (ORNL)

14
lib/gpu/lal_cg_cmm_long_ext.cpp → lib/gpu/lal_lj_sdk_long_ext.cpp
View File

@ -1,5 +1,5 @@
/*************************************************************************** /***************************************************************************
cg_cmm_long.h lj_sdk_long.h
------------------- -------------------
W. Michael Brown (ORNL) W. Michael Brown (ORNL)
@ -17,7 +17,7 @@
#include <cassert> #include <cassert>
#include <math.h> #include <math.h>
#include "lal_cg_cmm_long.h" #include "lal_lj_sdk_long.h"
using namespace std; using namespace std;
using namespace LAMMPS_AL; using namespace LAMMPS_AL;
@ -27,7 +27,7 @@ static CGCMMLong<PRECISION,ACC_PRECISION> CMMLMF;
// --------------------------------------------------------------------------- // ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device // 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_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj, double **host_lj4, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors, 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; return init_ok;
} }
void cmml_gpu_clear() { void sdkl_gpu_clear() {
CMMLMF.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, const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, tagint *tag, int **nspecial, double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag, 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); 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, double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag, int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start, 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); host_q,nlocal,boxlo,prd);
} }
double cmml_gpu_bytes() { double sdkl_gpu_bytes() {
return CMMLMF.host_memory_usage(); return CMMLMF.host_memory_usage();
} }

2
src/Depend.sh
View File

@ -109,7 +109,7 @@ if (test $1 = "RIGID") then
depend USER-OMP depend USER-OMP
fi fi
if (test $1 = "USER-CG-CMM") then if (test $1 = "USER-CGSDK") then
depend GPU depend GPU
depend KOKKOS depend KOKKOS
depend USER-OMP depend USER-OMP

20
src/GPU/pair_lj_sdk_coul_long_gpu.cpp
View File

@ -48,7 +48,7 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition // 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_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj, double **host_lj4, double **offset, double *special_lj,
const int nlocal, const int nall, const int max_nbors, 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, FILE *screen, double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e, double *host_special_coul, const double qqrd2e,
const double g_ewald); const double g_ewald);
void cmml_gpu_clear(); void sdkl_gpu_clear();
int ** cmml_gpu_compute_n(const int ago, const int inum, const int nall, int ** sdkl_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo, double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag, 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, int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo, bool &success, double *host_q, double *boxlo,
double *prd); 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, double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag, int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start, const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q, const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd); const int nlocal, double *boxlo, double *prd);
double cmml_gpu_bytes(); double sdkl_gpu_bytes();
#include "lj_sdk_common.h" #include "lj_sdk_common.h"
@ -95,7 +95,7 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) :
PairLJSDKCoulLongGPU::~PairLJSDKCoulLongGPU() PairLJSDKCoulLongGPU::~PairLJSDKCoulLongGPU()
{ {
cmml_gpu_clear(); sdkl_gpu_clear();
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -112,7 +112,7 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag)
int *ilist, *numneigh, **firstneigh; int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) { if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal; 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->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special, atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom, eflag, vflag, eflag_atom, vflag_atom,
@ -124,7 +124,7 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag)
ilist = list->ilist; ilist = list->ilist;
numneigh = list->numneigh; numneigh = list->numneigh;
firstneigh = list->firstneigh; 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, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q, vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd); atom->nlocal, domain->boxlo, domain->prd);
@ -185,7 +185,7 @@ void PairLJSDKCoulLongGPU::init_style()
int maxspecial=0; int maxspecial=0;
if (atom->molecular) if (atom->molecular)
maxspecial=atom->maxspecial; 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, lj4, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial, atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq, cell_size, gpu_mode, screen, cut_ljsq,
@ -205,7 +205,7 @@ void PairLJSDKCoulLongGPU::init_style()
double PairLJSDKCoulLongGPU::memory_usage() double PairLJSDKCoulLongGPU::memory_usage()
{ {
double bytes = Pair::memory_usage(); double bytes = Pair::memory_usage();
return bytes + cmml_gpu_bytes(); return bytes + sdkl_gpu_bytes();
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

1
src/GPU/pair_lj_sdk_coul_long_gpu.h
View File

@ -14,7 +14,6 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
PairStyle(lj/sdk/coul/long/gpu,PairLJSDKCoulLongGPU) PairStyle(lj/sdk/coul/long/gpu,PairLJSDKCoulLongGPU)
PairStyle(cg/cmm/coul/long/gpu,PairLJSDKCoulLongGPU)
#else #else

20
src/GPU/pair_lj_sdk_gpu.cpp
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@ -39,26 +39,26 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition // 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_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj, double **host_lj4, double **offset, double *special_lj,
const int nlocal, const int nall, const int max_nbors, const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode, const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen); FILE *screen);
void cmm_gpu_clear(); void sdk_gpu_clear();
int ** cmm_gpu_compute_n(const int ago, const int inum, const int nall, int ** sdk_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo, double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag, tagint **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start, const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, int **ilist, int **jnum,
const double cpu_time, bool &success); 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, double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag, int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start, const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success); const double cpu_time, bool &success);
double cmm_gpu_bytes(); double sdk_gpu_bytes();
#include "lj_sdk_common.h" #include "lj_sdk_common.h"
@ -80,7 +80,7 @@ PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE)
PairLJSDKGPU::~PairLJSDKGPU() PairLJSDKGPU::~PairLJSDKGPU()
{ {
cmm_gpu_clear(); sdk_gpu_clear();
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -97,7 +97,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag)
int *ilist, *numneigh, **firstneigh; int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) { if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal; 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->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special, atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom, eflag, vflag, eflag_atom, vflag_atom,
@ -108,7 +108,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag)
ilist = list->ilist; ilist = list->ilist;
numneigh = list->numneigh; numneigh = list->numneigh;
firstneigh = list->firstneigh; 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, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success); vflag_atom, host_start, cpu_time, success);
} }
@ -154,7 +154,7 @@ void PairLJSDKGPU::init_style()
int maxspecial=0; int maxspecial=0;
if (atom->molecular) if (atom->molecular)
maxspecial=atom->maxspecial; 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, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial, atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen); cell_size, gpu_mode, screen);
@ -172,7 +172,7 @@ void PairLJSDKGPU::init_style()
double PairLJSDKGPU::memory_usage() double PairLJSDKGPU::memory_usage()
{ {
double bytes = Pair::memory_usage(); double bytes = Pair::memory_usage();
return bytes + cmm_gpu_bytes(); return bytes + sdk_gpu_bytes();
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

1
src/GPU/pair_lj_sdk_gpu.h
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@ -14,7 +14,6 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
PairStyle(lj/sdk/gpu,PairLJSDKGPU) PairStyle(lj/sdk/gpu,PairLJSDKGPU)
PairStyle(cg/cmm/gpu,PairLJSDKGPU)
#else #else

2
src/Makefile
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@ -57,7 +57,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
mpiio mscg opt peri poems \ mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap srd voronoi 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-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-mgpt user-misc user-molfile \ user-intel user-lb user-manifold user-mgpt user-misc user-molfile \
user-nc-dump user-omp user-phonon user-qmmm user-qtb \ user-nc-dump user-omp user-phonon user-qmmm user-qtb \

0
src/USER-CG-CMM/Install.sh → src/USER-CGSDK/Install.sh
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22
src/USER-CG-CMM/README → src/USER-CGSDK/README
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@ -13,23 +13,15 @@ lipids and charged amino acids.
See the doc pages for these commands for details. See the doc pages for these commands for details.
There are example scripts for using this package in 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 This is the second generation implementation reducing the the clutter
of the previous version. For many systems with long range of the previous version. For many systems with long range
electrostatics, it will be faster to use pair_style hybrid/overlay 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 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 style, since the number of charged atom types is usually small.
exploit this property, the use of the kspace_style pppm/cg is To exploit this property, the use of the kspace_style pppm/cg is
recommended over regular pppm. For all new styles, input file backward recommended over regular pppm.
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.
The person who created this package is Axel Kohlmeyer at Temple U The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions. (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 Thanks for contributions, support and testing goes to
Wataru Shinoda (AIST, Tsukuba) Wataru Shinoda (Nagoya University)
Russell DeVane (Procter & Gamble) Russell DeVane (Procter & Gamble)
Michael L. Klein (CMM / U Penn, Philadelphia) Michael L. Klein (Temple University, Philadelphia)
Balasubramanian Sundaram (JNCASR, Bangalore) Balasubramanian Sundaram (JNCASR, Bangalore)
version: 0.99 / 2011-11-29 version: 1.0 / 2017-04-26

0
src/USER-CG-CMM/angle_sdk.cpp → src/USER-CGSDK/angle_sdk.cpp
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1
src/USER-CG-CMM/angle_sdk.h → src/USER-CGSDK/angle_sdk.h
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@ -14,7 +14,6 @@
#ifdef ANGLE_CLASS #ifdef ANGLE_CLASS
AngleStyle(sdk,AngleSDK) AngleStyle(sdk,AngleSDK)
AngleStyle(cg/cmm,AngleSDK)
#else #else

0
src/USER-CG-CMM/lj_sdk_common.h → src/USER-CGSDK/lj_sdk_common.h
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0
src/USER-CG-CMM/pair_lj_sdk.cpp → src/USER-CGSDK/pair_lj_sdk.cpp
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1
src/USER-CG-CMM/pair_lj_sdk.h → src/USER-CGSDK/pair_lj_sdk.h
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@ -18,7 +18,6 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
PairStyle(lj/sdk,PairLJSDK) PairStyle(lj/sdk,PairLJSDK)
PairStyle(cg/cmm,PairLJSDK)
#else #else

0
src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp → src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
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1
src/USER-CG-CMM/pair_lj_sdk_coul_long.h → src/USER-CGSDK/pair_lj_sdk_coul_long.h
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@ -18,7 +18,6 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
PairStyle(lj/sdk/coul/long,PairLJSDKCoulLong) PairStyle(lj/sdk/coul/long,PairLJSDKCoulLong)
PairStyle(cg/cmm/coul/long,PairLJSDKCoulLong)
#else #else

0
src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp → src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp
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1
src/USER-CG-CMM/pair_lj_sdk_coul_msm.h → src/USER-CGSDK/pair_lj_sdk_coul_msm.h
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@ -18,7 +18,6 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
PairStyle(lj/sdk/coul/msm,PairLJSDKCoulMSM) PairStyle(lj/sdk/coul/msm,PairLJSDKCoulMSM)
PairStyle(cg/cmm/coul/msm,PairLJSDKCoulMSM)
#else #else

1
src/USER-OMP/angle_sdk_omp.h
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@ -18,7 +18,6 @@
#ifdef ANGLE_CLASS #ifdef ANGLE_CLASS
AngleStyle(sdk/omp,AngleSDKOMP) AngleStyle(sdk/omp,AngleSDKOMP)
AngleStyle(cg/cmm/omp,AngleSDKOMP)
#else #else

1
src/USER-OMP/pair_lj_sdk_coul_long_omp.h
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@ -18,7 +18,6 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
PairStyle(lj/sdk/coul/long/omp,PairLJSDKCoulLongOMP) PairStyle(lj/sdk/coul/long/omp,PairLJSDKCoulLongOMP)
PairStyle(cg/cmm/coul/long/omp,PairLJSDKCoulLongOMP)
#else #else

1
src/USER-OMP/pair_lj_sdk_coul_msm_omp.h
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@ -18,7 +18,6 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
PairStyle(lj/sdk/coul/msm/omp,PairLJSDKCoulMSMOMP) PairStyle(lj/sdk/coul/msm/omp,PairLJSDKCoulMSMOMP)
PairStyle(cg/cmm/coul/msm/omp,PairLJSDKCoulMSMOMP)
#else #else

1
src/USER-OMP/pair_lj_sdk_omp.h
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@ -18,7 +18,6 @@
#ifdef PAIR_CLASS #ifdef PAIR_CLASS
PairStyle(lj/sdk/omp,PairLJSDKOMP) PairStyle(lj/sdk/omp,PairLJSDKOMP)
PairStyle(cg/cmm/omp,PairLJSDKOMP)
#else #else