diff --git a/src/USER-CG-CMM/Install.sh b/src/USER-CG-CMM/Install.sh index 83298b72fa..2e56ff545e 100644 --- a/src/USER-CG-CMM/Install.sh +++ b/src/USER-CG-CMM/Install.sh @@ -6,11 +6,17 @@ if (test $1 = 1) then if (test -e ../angle_harmonic.cpp) then cp angle_cg_cmm.h .. cp angle_cg_cmm.cpp .. + + cp angle_sdk.h .. + cp angle_sdk.cpp .. fi if (test -e ../pppm.cpp) then cp pair_cg_cmm_coul_long.cpp .. cp pair_cg_cmm_coul_long.h .. + + cp pair_lj_sdk_coul_long.cpp .. + cp pair_lj_sdk_coul_long.h .. fi cp cg_cmm_parms.h .. @@ -23,6 +29,10 @@ if (test $1 = 1) then cp pair_cg_cmm_coul_cut.cpp .. cp pair_cg_cmm_coul_cut.h .. + cp pair_lj_sdk.cpp .. + cp pair_lj_sdk.h .. + cp lj_sdk_common.h .. + elif (test $1 = 0) then rm -f ../angle_cg_cmm.h @@ -41,4 +51,13 @@ elif (test $1 = 0) then rm -f ../pair_cg_cmm_coul_long.cpp rm -f ../pair_cg_cmm_coul_long.h + rm -f ../lj_sdk_common.h + + rm -f ../angle_sdk.h + rm -f ../angle_sdk.cpp + + rm -f ../pair_lj_sdk.cpp + rm -f ../pair_lj_sdk.h + rm -f ../pair_lj_sdk_coul_long.cpp + rm -f ../pair_lj_sdk_coul_long.h fi diff --git a/src/USER-CG-CMM/Package.sh b/src/USER-CG-CMM/Package.sh index dcf6a81581..db51eed742 100644 --- a/src/USER-CG-CMM/Package.sh +++ b/src/USER-CG-CMM/Package.sh @@ -15,6 +15,18 @@ for file in *.cpp *.h; do if (test $file = pair_cg_cmm_coul_long.h -a ! -e ../pair_lj_cut_coul_long.h) then continue fi + if (test $file = angle_sdk.cpp -a ! -e ../pair_angle_harmonic.cpp) then + continue + fi + if (test $file = angle_sdk.h -a ! -e ../pair_angle_harmonic.h) then + continue + fi + if (test $file = pair_lj_sdk_coul_long.cpp -a ! -e ../pair_lj_cut_coul_long.cpp) then + continue + fi + if (test $file = pair_lj_sdk_coul_long.h -a ! -e ../pair_lj_cut_coul_long.h) then + continue + fi if (test ! -e ../$file) then echo " creating src/$file" diff --git a/src/USER-CG-CMM/README b/src/USER-CG-CMM/README index e93e739b12..b37fbd3760 100644 --- a/src/USER-CG-CMM/README +++ b/src/USER-CG-CMM/README @@ -1,25 +1,35 @@ -This package implements 4 commands which can be used in a LAMMPS input +This package implements 3 commands which can be used in a LAMMPS input script: -pair_style cg/cmm -pair_style cg/cmm/coul/cut -pair_style cg/cmm/coul/long -angle_style cg/cmm :ul +pair_style lj/sdk +pair_style lj/sdk/coul/long +angle_style sdk These styles allow coarse grained MD simulations with the parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) -(cg/cmm), with extensions to simulate ionic liquids, electrolytes, -lipids and charged amino acids (to be published soon). +(SDK), with extensions to simulate ionic liquids, electrolytes, +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. +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 and well, but there will be -optimizations, cleanups and additional tools to aid in setting up and -analyzing simulations with this package added in the next months. +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 (akohlmey at gmail.com). Contact him directly if you have questions. @@ -29,8 +39,8 @@ The person who created this package is Axel Kohlmeyer at Temple U Thanks for contributions, support and testing goes to Wataru Shinoda (AIST, Tsukuba) -Russell DeVane (CMM / U Penn, Philadelphia) -Balasubramanian Sundaram (JNCASR, Bangalore) +Russell DeVane (Procter & Gamble) Michael L. Klein (CMM / U Penn, Philadelphia) +Balasubramanian Sundaram (JNCASR, Bangalore) -version: 0.98 / 2008-01-31 +version: 0.99 / 2011-11-29 diff --git a/src/USER-CG-CMM/angle_cg_cmm.h b/src/USER-CG-CMM/angle_cg_cmm.h index 7fef95d5a8..5060415842 100644 --- a/src/USER-CG-CMM/angle_cg_cmm.h +++ b/src/USER-CG-CMM/angle_cg_cmm.h @@ -13,7 +13,7 @@ #ifdef ANGLE_CLASS -AngleStyle(cg/cmm,AngleCGCMM) +AngleStyle(cg/cmm/old,AngleCGCMM) #else diff --git a/src/USER-CG-CMM/pair_cg_cmm.h b/src/USER-CG-CMM/pair_cg_cmm.h index 27eb4d830a..74eee884e3 100644 --- a/src/USER-CG-CMM/pair_cg_cmm.h +++ b/src/USER-CG-CMM/pair_cg_cmm.h @@ -13,7 +13,7 @@ #ifdef PAIR_CLASS -PairStyle(cg/cmm,PairCGCMM) +PairStyle(cg/cmm/old,PairCGCMM) #else diff --git a/src/USER-CG-CMM/pair_cg_cmm_coul_cut.h b/src/USER-CG-CMM/pair_cg_cmm_coul_cut.h index 1309bec6d0..2732fa4d52 100644 --- a/src/USER-CG-CMM/pair_cg_cmm_coul_cut.h +++ b/src/USER-CG-CMM/pair_cg_cmm_coul_cut.h @@ -13,7 +13,7 @@ #ifdef PAIR_CLASS -PairStyle(cg/cmm/coul/cut,PairCGCMMCoulCut) +PairStyle(cg/cmm/coul/cut/old,PairCGCMMCoulCut) #else diff --git a/src/USER-CG-CMM/pair_cg_cmm_coul_long.h b/src/USER-CG-CMM/pair_cg_cmm_coul_long.h index d3fd0b453d..7bc15a853c 100644 --- a/src/USER-CG-CMM/pair_cg_cmm_coul_long.h +++ b/src/USER-CG-CMM/pair_cg_cmm_coul_long.h @@ -13,7 +13,7 @@ #ifdef PAIR_CLASS -PairStyle(cg/cmm/coul/long,PairCGCMMCoulLong) +PairStyle(cg/cmm/coul/long/old,PairCGCMMCoulLong) #else