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Revision	9592875e3995bb155fa1a65c503595c5fe3cecb2 (tree)
Zeit	2013-11-01 16:21:14
Autor	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

Ändern Zusammenfassung

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

Diff

--- a/doc/README.txt

+++ b/doc/README.txt

		@@ -87,7 +87,7 @@ COMPILE(using GNUmake):
87	87	Then, just type:
88	88	$ make -f Makefile_GNU
89	89
90		- For all case, the compile succeeded if you could fine "MolDS.out" in the "src" directory.
	90	+ For all case, the compile succeeded if you could fine "molds" in the "src" directory.
91	91	If you want to clean the compilation, type
92	92	$ make clean
93	93	If you want to compile MolDS in debug-mode,

		@@ -100,22 +100,22 @@ CARRY OUT MolDS:
100	100	After the compile, in the "src" directory,
101	101
102	102	For the calculations with single process:
103		- $ ./MolDS.out < input.in
	103	+ $ ./molds < input.in
104	104	or
105		- $ ./MolDS.out input.in
	105	+ $ ./molds input.in
106	106
107	107	For the calculations with muliple threads, type
108	108	$ export OMP_NUM_THREADS=n1
109		- $ ./MolDS.out input.in
	109	+ $ ./molds input.in
110	110	, where n1 is the number of threads.
111	111
112	112	For the calculations with multiple processes by MPI:
113		- $ mpirun -np n2 MolDS.out input.in
	113	+ $ mpirun -np n2 molds input.in
114	114	, where n2 after the "-np" is the number of process.
115	115
116	116	For the calculations with muliple threads and muliple processes, type
117	117	$ export OMP_NUM_THREADS=n1
118		- $ mpirun -np n2 MolDS.out input.in
	118	+ $ mpirun -np n2 molds input.in
119	119	, where n1 is the number of cores of each node and n2 is the number of nodes.
120	120
121	121	In the multiple processes calculations, process-0 can only output results.

		@@ -126,7 +126,7 @@ CARRY OUT MolDS:
126	126	namely,
127	127	$ make CFLAGS="-DMOLDS_DBG"
128	128	$ export OMP_NUM_THREADS=n1
129		- $ mpirun -np n2 MolDS.out input.in > /localFileSyste/output.dat
	129	+ $ mpirun -np n2 molds input.in > /localFileSyste/output.dat
130	130	, where n1 is the number of cores of each node and n2 is the number of nodes.
131	131
132	132	==============================================================================

--- a/src/Makefile

+++ b/src/Makefile

		@@ -33,7 +33,7 @@ LIBS = -lmkl_intel_ilp64 $(LIBSBASE) $(BOOST_LIBS)
33	33	else
34	34	LIBS = -lmkl_intel $(LIBSBASE) $(BOOST_LIBS)
35	35	endif
36		-EXENAME = MolDS.out
	36	+EXENAME = molds
37	37	DEPFILE = obj/objfile.dep
38	38	LDFLAGS =
39	39

--- a/src/Makefile_GNU

+++ b/src/Makefile_GNU

		@@ -30,7 +30,7 @@ OPENBLAS_LIB_DIR = $(OPENBLAS_TOP_DIR)lib/
30	30	OPENBLAS_LIBS = -lopenblas
31	31	LIBSBASE = -lpthread -lgomp
32	32	LIBS = $(LIBSBASE) $(BOOST_LIBS) $(OPENBLAS_LIBS)
33		-EXENAME = MolDS.out
	33	+EXENAME = molds
34	34	DEPFILE = obj/objfile.dep
35	35	LDFLAGS =
36	36

--- a/src/base/atoms/Satom.cpp

+++ b/src/base/atoms/Satom.cpp

		@@ -89,14 +89,24 @@ void Satom::SetAtomicParameters(){
89	89	this->indoG1CoefficientP = 0.0;
90	90	this->indoF2CoefficientS = 0.0;
91	91	this->indoF2CoefficientP = 0.0;
92		- // the zindoBondingParameterS for sulfer atoms are set to be equal
93		- // to the one (10.09eV) in "ORCA 2.8"( http://www.thch.uni-bonn.de/tc/orca/ ).
	92	+ // ORCA parameter set
	93	+ // see "ORCA 2.8"( http://www.thch.uni-bonn.de/tc/orca/ ).
94	94	//this->zindoBondingParameterS = -15.0*Parameters::GetInstance()->GetEV2AU();
	95	+ //this->zindoBondingParameterD = 0.0*Parameters::GetInstance()->GetEV2AU();
	96	+ //this->zindoF0ss = 10.09 * Parameters::GetInstance()->GetEV2AU();
	97	+ //this->zindoF0sd = 0.0;
	98	+ //this->zindoF0dd = 0.0;
	99	+ //this->zindoG1sp = 3.0756 * Parameters::GetInstance()->GetEV2AU();
	100	+ //this->zindoF2pp = 4.5377 * Parameters::GetInstance()->GetEV2AU();
	101	+ //this->zindoG2sd = 0.0;
	102	+ //this->zindoG1pd = 0.0;
	103	+ //this->zindoF2pd = 0.0;
	104	+ //this->zindoG3pd = 0.0;
	105	+ //this->zindoF2dd = 0.0;
	106	+ //this->zindoF4dd = 0.0;
	107	+ // end (ORCA parameter set)
95	108	this->zindoBondingParameterS = -14.0*Parameters::GetInstance()->GetEV2AU();
96	109	this->zindoBondingParameterD = 4.0*Parameters::GetInstance()->GetEV2AU();
97		- // the zindoF0ss for sulfer atoms are set to be equal
98		- // to the one (10.09eV) in "ORCA 2.8"( http://www.thch.uni-bonn.de/tc/orca/ ).
99		- //this->zindoF0ss = 10.09 * Parameters::GetInstance()->GetEV2AU();
100	110	this->zindoF0ss = 8.96 * Parameters::GetInstance()->GetEV2AU();
101	111	this->zindoF0sd = 0.0;
102	112	this->zindoF0dd = 0.0;

--- a/src/wrappers/Lapack.cpp

+++ b/src/wrappers/Lapack.cpp

		@@ -37,6 +37,7 @@
37	37	#include"mkl.h"
38	38	#elif defined __FCC_VERSION
39	39	#include"lapacke.h"
	40	+#include"mkl_lapacke.h"
40	41	#else
41	42	#if ( __WORDSIZE == 32 )
42	43	#else

--- a/test/Test_Of_MolDS.rb

+++ b/test/Test_Of_MolDS.rb

		@@ -21,7 +21,7 @@
21	21
22	22	Dir.chdir(File.dirname(__FILE__))
23	23
24		-MolDSBin = "../src/MolDS.out".freeze
	24	+MolDSBin = "../src/molds".freeze
25	25
26	26	module AllInclude
27	27	def include? *arg

		@@ -123,7 +123,7 @@ puts <<EOS
123	123	*****************************************
124	124	EOS
125	125
126		-puts 'MD5 sum of the MolDS.out to be tested:'
	126	+puts 'MD5 sum of the molds to be tested:'
127	127	system "md5sum #{MolDSBin}"
128	128	puts '',''
129	129

--- a/test/c2h6_mndo_directCIS_singlet_force_heap_limit.dat

+++ b/test/c2h6_mndo_directCIS_singlet_force_heap_limit.dat

		@@ -1,6 +1,6 @@
1	1
2	2
3		- >>>>> Welcome to the MolDS world at 2013/6/3(Mon.) 11:50:29 <<<<<
	3	+ >>>>> Welcome to the MolDS world at 2013/11/1(Fri.) 16:15:35 <<<<<
4	4
5	5
6	6	******** START: Parse input ********

		@@ -70,32 +70,33 @@ Error in base::MallocerFreer::Malloc: Reaches limit of heap. Change the "limit_h
70	70	Current Heap: 0.091712[MB].
71	71	Required Heap: 0.131072[MB].
72	72
	73	+key value pairs:
73	74	backtrace:
74		-../src/MolDS.out(_ZN10MolDS_base14MolDSException12GetBacktraceEi+0x2f)[0x430f0f]
75		-../src/MolDS.out(_ZN10MolDS_base14MolDSExceptionC2ESs+0x42)[0x431052]
76		-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer14CheckLimitHeapEd+0x150)[0x440840]
77		-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPT_m+0x4a)[0x45a0aa]
78		-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPT_mm+0xbd)[0x45a2ed]
79		-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPT_mmm+0xbb)[0x4760eb]
80		-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPT_mmmm+0x8a)[0x4a0aca]
81		-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPPT_mmmmm+0x98)[0x4e3368]
82		-../src/MolDS.out(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPPPT_mmmmmm+0xb5)[0x4e36e5]
83		-../src/MolDS.out(_ZN10MolDS_mndo4Mndo11SetMoleculeEPN10MolDS_base8MoleculeE+0x79)[0x4d95d9]
84		-../src/MolDS.out(_ZN8MolDS_md2MD4DoMDEv+0xe0)[0x4eba20]
85		-../src/MolDS.out(_ZNK10MolDS_base5MolDS4DoMDEPNS_8MoleculeEPb+0xb6)[0x50dac6]
86		-../src/MolDS.out(_ZN10MolDS_base5MolDS3RunEiPPc+0x46e)[0x50e62e]
87		-../src/MolDS.out(main+0x85)[0x430085]
88		-/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)[0x7f48d980eead]
89		-../src/MolDS.out[0x430b49]
	75	+ ./molds(_ZN10MolDS_base14MolDSException12GetBacktraceEi+0x61) [0x4a3cc1]
	76	+ ./molds(_ZN10MolDS_base14MolDSExceptionC1ESs+0xb2) [0x4a2d4a]
	77	+ ./molds(_ZNK10MolDS_base13MallocerFreer14CheckLimitHeapEd+0x2e5) [0x4b2dcf]
	78	+ ./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPT_m+0x58) [0x4b942c]
	79	+ ./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPT_mm+0xc1) [0x4b8fdd]
	80	+ ./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPT_mmm+0xda) [0x51822e]
	81	+ ./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPT_mmmm+0xf3) [0x517ba7]
	82	+ ./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPPT_mmmmm+0x102) [0x58bba2]
	83	+ ./molds(_ZNK10MolDS_base13MallocerFreer6MallocIdEEvPPPPPPPT_mmmmmm+0x10e) [0x58b47a]
	84	+ ./molds(_ZN10MolDS_mndo4Mndo11SetMoleculeEPN10MolDS_base8MoleculeE+0xc1) [0x58dba1]
	85	+ ./molds(_ZN8MolDS_md2MD4DoMDEv+0x14c) [0x5d2c72]
	86	+ ./molds(_ZNK10MolDS_base5MolDS4DoMDEPNS_8MoleculeEPb+0x16e) [0x5f0c8c]
	87	+ ./molds(_ZN10MolDS_base5MolDS3RunEiPPc+0x394) [0x5f0094]
	88	+ ./molds(main+0x6e2) [0x5f2ff6]
	89	+ /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f234416d76d]
	90	+ ./molds() [0x48f4f9]
90	91	Summary for memory usage:
91	92	Max Heap: 0.091712[MB].
92	93	Current Heap(Leaked): 0.000000[MB].
93	94
94	95
95	96	>>>>> The MolDS finished abnormally.............. <<<<<
96		- >>>>> CPU time: 0.01[s]. <<<<<
	97	+ >>>>> CPU time: 0[s]. <<<<<
97	98	>>>>> Elapsed time: 0[s]. <<<<<
98		- >>>>> Elapsed time(OMP): 0.00183718[s]. <<<<<
	99	+ >>>>> Elapsed time(OMP): 0.00606799[s]. <<<<<
99	100	>>>>> See you. <<<<<
100	101
101	102

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