Commit: ca19512b8d44e51261398ed395795d25f37e8871 - MolDS (git)

Commit MetaInfo

• Révision: ca19512b8d44e51261398ed395795d25f37e8871 (tree)
• l'heure: 2013-12-20 19:20:37
• Auteur: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Message de Log

Revert to development mode to start version 0.4.0

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/trunk@1587 1136aad2-a195-0410-b898-f5ea1d11b9d8

Change Summary

• modified: doc/README.txt
• modified: src/Main.cpp
• modified: src/Makefile
• modified: src/Makefile_GNU

Modification

--- a/doc/README.txt
+++ b/doc/README.txt
@@ -22,7 +22,7 @@
 ==============================================================================
 
 
-   MolDS ("Mol"ecular "D"ynamics "S"imulation package) ver. 0.3.0
+   MolDS ("Mol"ecular "D"ynamics "S"imulation package) ver. 0.4.0 (Under developement)
       developed by Mikiya Fujii, Ph.D., Katsuhiko Nishimra, and Michihiro Okuyama, Ph.D..
       For Questions and bug reports: [e-mail]
 
@@ -343,6 +343,46 @@ HOW TO WRITE INPUT:
             file_prefix MOPlot_
          MOPLOT_END
 
+   <Environmental Point Charge(EPC) method>
+      Environmental point charge method is a simplified method of the QM/MM,
+      namely the environmental point changes are treated as atoms in the MM region.
+      The differences between the QM/MM and EPC are summarized below:
+         - Electrostatic interaction between QM and MM region:
+            QM/MM: Electrostatic interaction may be mutually added to QM and MM atoms.
+            EPC  : Electrostatic field caused by the EPCs affects the QM region
+                   although the each EPC is not affected by electrostatic field 
+                   caused by the QM atoms and other EPCs. 
+                   Namely, each EPC is fixed at point of space.
+         - Van der Waals interaction between QM and MM region:
+            QM/MM: Included.
+            EPC  : Not included.
+      In this EPC method, core-core replustion between QM and MM atoms is implemented with
+      the method I (simple coulomb interaction: qq/r) of ref [LRCL_2000].
+      This EPC method can be used with MNDO-series (MNDO, AM1, AM1-D, PM3, PM3-D, and PDDG/PM3) only.
+      To use this environmental point charges method, write EPC-directive. 
+
+      E.g.
+         EPC
+            (options)
+         EPC_END
+      
+      -options
+       "the cartesian coordinates and charge" is only prepared.
+       Namely, each line should containe 4 doubles and a term. 
+       The first three doubles are the cartesian coordinates of 
+       each environmental point charge in angstrom unit.
+       The term is "charge". The last double following the term, "charge", 
+       is the charge in atomic unit, 
+       e.g. -1 and 1 mean charge of an electron and a proton, respectively.
+       Multiple setting of the environmental point charge is approvable, of course.
+
+       E.g. 
+         EPC 
+            0.0 0.0 0.0 charge -1   
+            2.2 1.5 3.0 charge -1.5
+            0.0 2.0 5.0 charge  0.3
+         EPC_END
+
    <Frequencies (Normal modes analysis)>
       write frequencies-directive. Note taht not only the frequencies but also the normal modes are calculated.
 

--- a/src/Main.cpp
+++ b/src/Main.cpp
@@ -40,8 +40,8 @@ using namespace MolDS_base;
 int main(int argc, char *argv[]){
    string optionHelp="-h";
    string optionVersion="-v";
-   string messageHelp="See README.txt: \"http://sourceforge.jp/projects/molds/scm/svn/blobs/head/tags/0.3.0/doc/README.txt\"\n";
-   string messageVersion="MolDS 0.3.0\n";
+   string messageHelp="See README.txt: \"http://sourceforge.jp/projects/molds/scm/svn/tree/head/trunk/doc/\"\n";
+   string messageVersion="MolDS 0.4.0(Under development)\n";
    for(int i=0; i<argc; i++){
       if(optionHelp.compare(argv[i])==0){
          std::cout << messageHelp;

--- a/src/Makefile
+++ b/src/Makefile
@@ -18,7 +18,7 @@
 #// along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
 #//************************************************************************//
 CC = mpiicpc
-CFLAGS = -O2
+CFLAGS = -O0
 override CFLAGS += -openmp -DMKL_INT=intptr_t
 ifeq ($(INTEL), 64)
 override CFLAGS += -DMKL_ILP64

--- a/src/Makefile_GNU
+++ b/src/Makefile_GNU
@@ -18,7 +18,7 @@
 #// along with MolDS.  If not, see <http://www.gnu.org/licenses/>.         // 
 #//************************************************************************//
 CC = mpicxx
-CFLAGS = -O2
+CFLAGS = -O0
 override CFLAGS += -fopenmp
 BOOST_TOP_DIR = /usr/local/boost/
 BOOST_INC_DIR = $(BOOST_TOP_DIR)/include/