git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7251 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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

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"

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 lj/sdk
-pair_style cg/cmm/coul/cut
+pair_style lj/sdk/coul/long
-pair_style cg/cmm/coul/long
+angle_style sdk
-angle_style cg/cmm :ul
 
 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,
+(SDK), with extensions to simulate ionic liquids, electrolytes,
-lipids and charged amino acids (to be published soon).
+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
+quality. The CG potentials work correctly for "normal" situations, but
-optimizations, cleanups and additional tools to aid in setting up and
+have not been testing with all kinds of potential parameters and
-analyzing simulations with this package added in the next months.
+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)
+Russell DeVane (Procter & Gamble)
-Balasubramanian Sundaram (JNCASR, Bangalore)
 Michael L. Klein (CMM / U Penn, Philadelphia)
+Balasubramanian Sundaram (JNCASR, Bangalore)
 
-version: 0.98 / 2008-01-31
+version: 0.99 / 2011-11-29

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
 

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
 

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
 

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