提交: 9592875e3995bb155fa1a65c503595c5fe3cecb2 - MolDS (git)

Commit MetaInfo

• 修订版: 9592875e3995bb155fa1a65c503595c5fe3cecb2 (tree)
• 时间: 2013-11-01 16:21:14
• 作者: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Log Message

trunk.r1557 is merged to branches/fx10. #32094 #32380

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/branches/fx10@1558 1136aad2-a195-0410-b898-f5ea1d11b9d8

更改概述

• modified: doc/README.txt
• modified: src/Makefile
• modified: src/Makefile_GNU
• modified: src/base/atoms/Satom.cpp
• modified: src/wrappers/Lapack.cpp
• modified: test/Test_Of_MolDS.rb
• modified: test/c2h6_mndo_directCIS_singlet_force_heap_limit.dat

差异

--- a/doc/README.txt
+++ b/doc/README.txt
@@ -87,7 +87,7 @@ COMPILE(using GNUmake):
       Then, just type: 
       $ make -f Makefile_GNU 
 
-   For all case, the compile succeeded if you could fine "MolDS.out" in the "src" directory. 
+   For all case, the compile succeeded if you could fine "molds" in the "src" directory. 
    If you want to clean the compilation, type 
    $ make clean
    If you want to compile MolDS in debug-mode, 
@@ -100,22 +100,22 @@ CARRY OUT MolDS:
    After the compile, in the "src" directory,
 
    For the calculations with single process:
-   $ ./MolDS.out < input.in
+   $ ./molds < input.in
    or
-   $ ./MolDS.out input.in
+   $ ./molds input.in
 
    For the calculations with muliple threads, type
    $ export OMP_NUM_THREADS=n1
-   $ ./MolDS.out input.in
+   $ ./molds input.in
    , where n1 is the number of threads.
 
    For the calculations with multiple processes by MPI:
-   $ mpirun -np n2 MolDS.out input.in
+   $ mpirun -np n2 molds input.in
    , where n2 after the "-np" is the number of process.
 
    For the calculations with muliple threads and muliple processes, type
    $ export OMP_NUM_THREADS=n1
-   $ mpirun -np n2 MolDS.out input.in
+   $ mpirun -np n2 molds input.in
    , where n1 is the number of cores of each node and n2 is the number of nodes.
 
    In the multiple processes calculations, process-0 can only output results.
@@ -126,7 +126,7 @@ CARRY OUT MolDS:
    namely, 
    $ make CFLAGS="-DMOLDS_DBG"
    $ export OMP_NUM_THREADS=n1
-   $ mpirun -np n2 MolDS.out input.in > /localFileSyste/output.dat
+   $ mpirun -np n2 molds input.in > /localFileSyste/output.dat
    , where n1 is the number of cores of each node and n2 is the number of nodes.
 
 ==============================================================================

--- a/src/Makefile
+++ b/src/Makefile
@@ -33,7 +33,7 @@ LIBS = -lmkl_intel_ilp64 $(LIBSBASE) $(BOOST_LIBS)
 else
 LIBS = -lmkl_intel       $(LIBSBASE) $(BOOST_LIBS)
 endif
-EXENAME = MolDS.out
+EXENAME = molds
 DEPFILE = obj/objfile.dep
 LDFLAGS =
 

--- a/src/Makefile_GNU
+++ b/src/Makefile_GNU
@@ -30,7 +30,7 @@ OPENBLAS_LIB_DIR = $(OPENBLAS_TOP_DIR)lib/
 OPENBLAS_LIBS    = -lopenblas
 LIBSBASE = -lpthread -lgomp
 LIBS = $(LIBSBASE) $(BOOST_LIBS) $(OPENBLAS_LIBS)
-EXENAME = MolDS.out
+EXENAME = molds
 DEPFILE = obj/objfile.dep
 LDFLAGS =
 

--- a/src/base/atoms/Satom.cpp
+++ b/src/base/atoms/Satom.cpp
@@ -89,14 +89,24 @@ void Satom::SetAtomicParameters(){
    this->indoG1CoefficientP = 0.0;
    this->indoF2CoefficientS = 0.0;
    this->indoF2CoefficientP = 0.0;
-   // the zindoBondingParameterS for sulfer atoms are set to be equal 
-   // to the one (10.09eV) in "ORCA 2.8"( http://www.thch.uni-bonn.de/tc/orca/ ).
+   // ORCA parameter set
+   // see "ORCA 2.8"( http://www.thch.uni-bonn.de/tc/orca/ ).
    //this->zindoBondingParameterS = -15.0*Parameters::GetInstance()->GetEV2AU();
+   //this->zindoBondingParameterD =   0.0*Parameters::GetInstance()->GetEV2AU();
+   //this->zindoF0ss = 10.09 * Parameters::GetInstance()->GetEV2AU(); 
+   //this->zindoF0sd = 0.0;                   
+   //this->zindoF0dd = 0.0;                 
+   //this->zindoG1sp = 3.0756 * Parameters::GetInstance()->GetEV2AU();                 
+   //this->zindoF2pp = 4.5377 * Parameters::GetInstance()->GetEV2AU();
+   //this->zindoG2sd = 0.0;
+   //this->zindoG1pd = 0.0;        
+   //this->zindoF2pd = 0.0;
+   //this->zindoG3pd = 0.0;
+   //this->zindoF2dd = 0.0;
+   //this->zindoF4dd = 0.0;
+   // end (ORCA parameter set)
    this->zindoBondingParameterS = -14.0*Parameters::GetInstance()->GetEV2AU();
    this->zindoBondingParameterD =   4.0*Parameters::GetInstance()->GetEV2AU();
-   // the zindoF0ss for sulfer atoms are set to be equal 
-   // to the one (10.09eV) in "ORCA 2.8"( http://www.thch.uni-bonn.de/tc/orca/ ).
-   //this->zindoF0ss = 10.09 * Parameters::GetInstance()->GetEV2AU(); 
    this->zindoF0ss = 8.96 * Parameters::GetInstance()->GetEV2AU();                  
    this->zindoF0sd = 0.0;                   
    this->zindoF0dd = 0.0;                 

--- a/src/wrappers/Lapack.cpp
+++ b/src/wrappers/Lapack.cpp
@@ -37,6 +37,7 @@
    #include"mkl.h"
 #elif defined __FCC_VERSION
    #include"lapacke.h"
+#include"mkl_lapacke.h"
 #else
    #if ( __WORDSIZE == 32 )
    #else

--- a/test/Test_Of_MolDS.rb
+++ b/test/Test_Of_MolDS.rb
@@ -21,7 +21,7 @@
 
 Dir.chdir(File.dirname(__FILE__))
 
-MolDSBin = "../src/MolDS.out".freeze
+MolDSBin = "../src/molds".freeze
 
 module AllInclude
 	def include? *arg
@@ -123,7 +123,7 @@ puts <<EOS
 *****************************************
 EOS
 
-puts 'MD5 sum of the MolDS.out to be tested:'
+puts 'MD5 sum of the molds to be tested:'
 system "md5sum #{MolDSBin}"
 puts '',''
 

--- a/test/c2h6_mndo_directCIS_singlet_force_heap_limit.dat
+++ b/test/c2h6_mndo_directCIS_singlet_force_heap_limit.dat
@@ -1,6 +1,6 @@
 
 
-     >>>>>  Welcome to the MolDS world at 2013/6/3(Mon.) 11:50:29  <<<<<
+     >>>>>  Welcome to the MolDS world at 2013/11/1(Fri.) 16:15:35  <<<<<
 
 
 **********  START: Parse input  **********
@@ -70,32 +70,33 @@ Error in base::MallocerFreer::Malloc: Reaches limit of heap. Change the "limit_h
 		Current Heap:  0.091712[MB].
 		Required Heap: 0.131072[MB].
 
+key value pairs:
 backtrace:
-../src/MolDS.out(_ZN10MolDS_base14MolDSException12GetBacktraceEi+0x2f)[0x430f0f]
-../src/MolDS.out(_ZN10MolDS_base14MolDSExceptionC2ESs+0x42)[0x431052]
-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer14CheckLimitHeapEd+0x150)[0x440840]
-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPT_m+0x4a)[0x45a0aa]
-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPT_mm+0xbd)[0x45a2ed]
-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPT_mmm+0xbb)[0x4760eb]
-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPT_mmmm+0x8a)[0x4a0aca]
-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPPT_mmmmm+0x98)[0x4e3368]
-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPPPT_mmmmmm+0xb5)[0x4e36e5]
-../src/MolDS.out(_ZN10MolDS_mndo4Mndo11SetMoleculeEPN10MolDS_base8MoleculeE+0x79)[0x4d95d9]
-../src/MolDS.out(_ZN8MolDS_md2MD4DoMDEv+0xe0)[0x4eba20]
-../src/MolDS.out(_ZNK10MolDS_base5MolDS4DoMDEPNS_8MoleculeEPb+0xb6)[0x50dac6]
-../src/MolDS.out(_ZN10MolDS_base5MolDS3RunEiPPc+0x46e)[0x50e62e]
-../src/MolDS.out(main+0x85)[0x430085]
-/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)[0x7f48d980eead]
-../src/MolDS.out[0x430b49]
+	./molds(_ZN10MolDS_base14MolDSException12GetBacktraceEi+0x61) [0x4a3cc1]
+	./molds(_ZN10MolDS_base14MolDSExceptionC1ESs+0xb2) [0x4a2d4a]
+	./molds(_ZNK10MolDS_base13MallocerFreer14CheckLimitHeapEd+0x2e5) [0x4b2dcf]
+	./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPT_m+0x58) [0x4b942c]
+	./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPT_mm+0xc1) [0x4b8fdd]
+	./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPT_mmm+0xda) [0x51822e]
+	./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPT_mmmm+0xf3) [0x517ba7]
+	./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPPT_mmmmm+0x102) [0x58bba2]
+	./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPPPT_mmmmmm+0x10e) [0x58b47a]
+	./molds(_ZN10MolDS_mndo4Mndo11SetMoleculeEPN10MolDS_base8MoleculeE+0xc1) [0x58dba1]
+	./molds(_ZN8MolDS_md2MD4DoMDEv+0x14c) [0x5d2c72]
+	./molds(_ZNK10MolDS_base5MolDS4DoMDEPNS_8MoleculeEPb+0x16e) [0x5f0c8c]
+	./molds(_ZN10MolDS_base5MolDS3RunEiPPc+0x394) [0x5f0094]
+	./molds(main+0x6e2) [0x5f2ff6]
+	/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f234416d76d]
+	./molds() [0x48f4f9]
 	Summary for memory usage:
 		Max Heap: 0.091712[MB].
 		Current Heap(Leaked): 0.000000[MB].
 
 
      >>>>>  The MolDS finished abnormally..............  <<<<<
-     >>>>>  CPU time: 0.01[s].  <<<<<
+     >>>>>  CPU time: 0[s].  <<<<<
      >>>>>  Elapsed time: 0[s].  <<<<<
-     >>>>>  Elapsed time(OMP): 0.00183718[s].  <<<<<
+     >>>>>  Elapsed time(OMP): 0.00606799[s].  <<<<<
      >>>>>  See you.  <<<<<