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root/OpenMD/trunk/src/applications/dynamicProps/DynamicProps.cpp

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 917 by tim, Fri Mar 24 17:29:07 2006 UTC vs.
Revision 1565 by chuckv, Thu May 19 14:28:04 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <iostream>
#	Line 53 | Line 53
53		#include "applications/dynamicProps/RCorrFunc.hpp"
54		#include "applications/dynamicProps/VCorrFunc.hpp"
55		#include "applications/dynamicProps/LegendreCorrFunc.hpp"
56	+	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
57	+	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
58	+	#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
59	+	#include "applications/dynamicProps/EnergyCorrFunc.hpp"
60	+	#include "applications/dynamicProps/StressCorrFunc.hpp"
61
62
63	<	using namespace oopse;
63	>	using namespace OpenMD;
64
65		int main(int argc, char* argv[]){
66
#	Line 72 | Line 77 | int main(int argc, char* argv[]){
77
78		//get the dumpfile name and meta-data file name
79		std::string dumpFileName = args_info.input_arg;
75	–
76	–	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
77	–
80
81		std::string sele1;
82		std::string sele2;
#	Line 82 | Line 84 | int main(int argc, char* argv[]){
84		if (args_info.sele1_given) {
85		sele1 = args_info.sele1_arg;
86		}else {
87	<	char*  sele1Env= getenv("OOPSE_SELE1");
87	>	char*  sele1Env= getenv("SELECTION1");
88		if (sele1Env) {
89		sele1 = sele1Env;
90		}else {
91		sprintf( painCave.errMsg,
92	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
93	<	painCave.severity = OOPSE_ERROR;
92	>	"neither --sele1 option nor $SELECTION1 is set");
93	>	painCave.severity = OPENMD_ERROR;
94		painCave.isFatal = 1;
95		simError();
96		}
#	Line 97 | Line 99 | int main(int argc, char* argv[]){
99		if (args_info.sele2_given) {
100		sele2 = args_info.sele2_arg;
101		}else {
102	<	char* sele2Env = getenv("OOPSE_SELE2");
102	>	char* sele2Env = getenv("SELECTION2");
103		if (sele2Env) {
104		sele2 = sele2Env;
105		} else {
#	Line 107 | Line 109 | int main(int argc, char* argv[]){
109
110		//parse md file and set up the system
111		SimCreator creator;
112	<	SimInfo* info = creator.createSim(mdFileName, false);
112	>	SimInfo* info = creator.createSim(dumpFileName, false);
113
114
115		TimeCorrFunc* corrFunc;
#	Line 115 | Line 117 | int main(int argc, char* argv[]){
117		corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
118		} else if (args_info.rcorr_given) {
119		corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
120	<	}
121	<	else if (args_info.vcorr_given) {
120	>	} else if (args_info.r_rcorr_given) {
121	>	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
122	>	} else if (args_info.thetacorr_given) {
123	>	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
124	>	} else if (args_info.drcorr_given) {
125	>	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
126	>	} else if (args_info.vcorr_given) {
127		corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
128	+	} else if (args_info.helfandEcorr_given){
129	+	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2);
130	+	} else if (args_info.StresCorrFunc_given){
131	+	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2);
132		} else if (args_info.lcorr_given) {
133		int order;
134		if (args_info.order_given)
#	Line 125 | Line 136 | int main(int argc, char* argv[]){
136		else {
137		sprintf( painCave.errMsg,
138		"--order must be set if --lcoor is set\n");
139	<	painCave.severity = OOPSE_ERROR;
139	>	painCave.severity = OPENMD_ERROR;
140		painCave.isFatal = 1;
141		simError();
142		}

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 917 by tim, Fri Mar 24 17:29:07 2006 UTC vs.
Revision 1565 by chuckv, Thu May 19 14:28:04 2011 UTC

#	Line 0 | Line 1
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