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). |
39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
41 |
|
*/ |
42 |
|
|
43 |
|
#include <iostream> |
44 |
|
#include <fstream> |
45 |
|
#include <string> |
46 |
|
|
46 |
– |
#include "brains/Register.hpp" |
47 |
|
#include "brains/SimCreator.hpp" |
48 |
|
#include "brains/SimInfo.hpp" |
49 |
|
#include "io/DumpReader.hpp" |
57 |
|
#include "applications/staticProps/GofRAngle.hpp" |
58 |
|
#include "applications/staticProps/GofAngle2.hpp" |
59 |
|
#include "applications/staticProps/GofXyz.hpp" |
60 |
+ |
#include "applications/staticProps/TwoDGofR.hpp" |
61 |
|
#include "applications/staticProps/P2OrderParameter.hpp" |
62 |
|
#include "applications/staticProps/BondOrderParameter.hpp" |
63 |
|
#include "applications/staticProps/BOPofR.hpp" |
64 |
|
#include "applications/staticProps/RippleOP.hpp" |
65 |
|
#include "applications/staticProps/SCDOrderParameter.hpp" |
66 |
|
#include "applications/staticProps/DensityPlot.hpp" |
67 |
+ |
#include "applications/staticProps/ObjectCount.hpp" |
68 |
|
#include "applications/staticProps/RhoZ.hpp" |
69 |
|
#include "applications/staticProps/pAngle.hpp" |
70 |
|
#include "applications/staticProps/BondAngleDistribution.hpp" |
71 |
|
#include "applications/staticProps/NanoVolume.hpp" |
72 |
+ |
#include "applications/staticProps/NanoLength.hpp" |
73 |
|
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
74 |
|
#include "applications/staticProps/Hxy.hpp" |
75 |
|
#endif |
76 |
|
#include "applications/staticProps/RhoR.hpp" |
77 |
< |
|
77 |
> |
#include "applications/staticProps/AngleR.hpp" |
78 |
> |
#include "applications/staticProps/TetrahedralityParam.hpp" |
79 |
> |
#include "applications/staticProps/TetrahedralityParamZ.hpp" |
80 |
|
using namespace OpenMD; |
81 |
|
|
82 |
|
int main(int argc, char* argv[]){ |
83 |
|
|
84 |
< |
//register force fields |
85 |
< |
registerForceFields(); |
86 |
< |
|
87 |
< |
gengetopt_args_info args_info; |
88 |
< |
|
89 |
< |
//parse the command line option |
90 |
< |
if (cmdline_parser (argc, argv, &args_info) != 0) { |
91 |
< |
exit(1) ; |
92 |
< |
} |
93 |
< |
|
94 |
< |
//get the dumpfile name |
95 |
< |
std::string dumpFileName = args_info.input_arg; |
96 |
< |
std::string sele1; |
97 |
< |
std::string sele2; |
98 |
< |
bool userSpecifiedSelect1; |
99 |
< |
bool userSpecifiedSelect2; |
100 |
< |
|
101 |
< |
// check the first selection argument, or set it to the environment |
102 |
< |
// variable, or failing that, set it to "select all" |
103 |
< |
|
104 |
< |
if (args_info.sele1_given) { |
105 |
< |
sele1 = args_info.sele1_arg; |
84 |
> |
|
85 |
> |
gengetopt_args_info args_info; |
86 |
> |
|
87 |
> |
//parse the command line option |
88 |
> |
if (cmdline_parser (argc, argv, &args_info) != 0) { |
89 |
> |
exit(1) ; |
90 |
> |
} |
91 |
> |
|
92 |
> |
//get the dumpfile name |
93 |
> |
std::string dumpFileName = args_info.input_arg; |
94 |
> |
std::string sele1; |
95 |
> |
std::string sele2; |
96 |
> |
|
97 |
> |
// check the first selection argument, or set it to the environment |
98 |
> |
// variable, or failing that, set it to "select all" |
99 |
> |
|
100 |
> |
if (args_info.sele1_given) { |
101 |
> |
sele1 = args_info.sele1_arg; |
102 |
> |
} else { |
103 |
> |
char* sele1Env= getenv("SELECTION1"); |
104 |
> |
if (sele1Env) { |
105 |
> |
sele1 = sele1Env; |
106 |
|
} else { |
107 |
< |
char* sele1Env= getenv("SELECTION1"); |
103 |
< |
if (sele1Env) { |
104 |
< |
sele1 = sele1Env; |
105 |
< |
} else { |
106 |
< |
sele1 = "select all"; |
107 |
< |
} |
107 |
> |
sele1 = "select all"; |
108 |
|
} |
109 |
< |
|
110 |
< |
// check the second selection argument, or set it to the environment |
111 |
< |
// variable, or failing that, set it to "select all" |
109 |
> |
} |
110 |
|
|
111 |
< |
if (args_info.sele2_given) { |
112 |
< |
sele2 = args_info.sele2_arg; |
113 |
< |
} else { |
114 |
< |
char* sele2Env = getenv("SELECTION1"); |
115 |
< |
if (sele2Env) { |
116 |
< |
sele2 = sele2Env; |
117 |
< |
} else { |
118 |
< |
sele2 = "select all"; |
119 |
< |
} |
111 |
> |
// check the second selection argument, or set it to the environment |
112 |
> |
// variable, or failing that, set it to "select all" |
113 |
> |
|
114 |
> |
if (args_info.sele2_given) { |
115 |
> |
sele2 = args_info.sele2_arg; |
116 |
> |
} else { |
117 |
> |
char* sele2Env = getenv("SELECTION1"); |
118 |
> |
if (sele2Env) { |
119 |
> |
sele2 = sele2Env; |
120 |
> |
} else { |
121 |
> |
//It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior |
122 |
> |
//should not be 'select all' but rather what is already intended for sele1 |
123 |
> |
//JRM 8/22/12 |
124 |
> |
sele2 = sele1; |
125 |
> |
//sele2 = "select all"; |
126 |
|
} |
127 |
< |
|
128 |
< |
|
129 |
< |
// Problems if sele1 wasn't specified, but |
130 |
< |
// if (!args_info.scd_given) { |
131 |
< |
// sprintf( painCave.errMsg, |
132 |
< |
// "neither --sele1 option nor $SELECTION1 is set"); |
133 |
< |
// painCave.severity = OPENMD_ERROR; |
134 |
< |
// painCave.isFatal = 1; |
135 |
< |
// simError(); |
136 |
< |
// } |
137 |
< |
// } |
138 |
< |
|
139 |
< |
// Problems if sele1 wasn't specified |
140 |
< |
|
141 |
< |
// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) { |
142 |
< |
// sprintf( painCave.errMsg, |
143 |
< |
// "neither --sele2 option nor $SELECTION1 is set"); |
144 |
< |
// painCave.severity = OPENMD_ERROR; |
145 |
< |
// painCave.isFatal = 1; |
146 |
< |
// simError(); |
147 |
< |
// } |
148 |
< |
// } |
149 |
< |
|
150 |
< |
bool batchMode; |
151 |
< |
if (args_info.scd_given){ |
152 |
< |
if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) { |
153 |
< |
batchMode = false; |
154 |
< |
} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) { |
155 |
< |
if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) { |
156 |
< |
sprintf( painCave.errMsg, |
157 |
< |
"below conditions are not satisfied:\n" |
158 |
< |
"0 <= begin && 0<= end && begin <= end-2\n"); |
159 |
< |
painCave.severity = OPENMD_ERROR; |
160 |
< |
painCave.isFatal = 1; |
161 |
< |
simError(); |
162 |
< |
} |
163 |
< |
batchMode = true; |
164 |
< |
} else{ |
165 |
< |
sprintf( painCave.errMsg, |
166 |
< |
"either --sele1, --sele2, --sele3 are specified," |
167 |
< |
" or --molname, --begin, --end are specified\n"); |
168 |
< |
painCave.severity = OPENMD_ERROR; |
169 |
< |
painCave.isFatal = 1; |
170 |
< |
simError(); |
171 |
< |
|
172 |
< |
} |
127 |
> |
} |
128 |
> |
|
129 |
> |
|
130 |
> |
// Problems if sele1 wasn't specified, but |
131 |
> |
// if (!args_info.scd_given) { |
132 |
> |
// sprintf( painCave.errMsg, |
133 |
> |
// "neither --sele1 option nor $SELECTION1 is set"); |
134 |
> |
// painCave.severity = OPENMD_ERROR; |
135 |
> |
// painCave.isFatal = 1; |
136 |
> |
// simError(); |
137 |
> |
// } |
138 |
> |
// } |
139 |
> |
|
140 |
> |
// Problems if sele1 wasn't specified |
141 |
> |
|
142 |
> |
// if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) { |
143 |
> |
// sprintf( painCave.errMsg, |
144 |
> |
// "neither --sele2 option nor $SELECTION1 is set"); |
145 |
> |
// painCave.severity = OPENMD_ERROR; |
146 |
> |
// painCave.isFatal = 1; |
147 |
> |
// simError(); |
148 |
> |
// } |
149 |
> |
// } |
150 |
> |
|
151 |
> |
bool batchMode; |
152 |
> |
if (args_info.scd_given){ |
153 |
> |
if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) { |
154 |
> |
batchMode = false; |
155 |
> |
} else if (args_info.molname_given && args_info.begin_given && args_info.end_given) { |
156 |
> |
if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) { |
157 |
> |
sprintf( painCave.errMsg, |
158 |
> |
"below conditions are not satisfied:\n" |
159 |
> |
"0 <= begin && 0<= end && begin <= end-2\n"); |
160 |
> |
painCave.severity = OPENMD_ERROR; |
161 |
> |
painCave.isFatal = 1; |
162 |
> |
simError(); |
163 |
> |
} |
164 |
> |
batchMode = true; |
165 |
> |
} else{ |
166 |
> |
sprintf( painCave.errMsg, |
167 |
> |
"either --sele1, --sele2, --sele3 are specified," |
168 |
> |
" or --molname, --begin, --end are specified\n"); |
169 |
> |
painCave.severity = OPENMD_ERROR; |
170 |
> |
painCave.isFatal = 1; |
171 |
> |
simError(); |
172 |
> |
|
173 |
|
} |
174 |
+ |
} |
175 |
+ |
|
176 |
+ |
//parse md file and set up the system |
177 |
+ |
SimCreator creator; |
178 |
+ |
std::cout << "dumpFile = " << dumpFileName << "\n"; |
179 |
+ |
SimInfo* info = creator.createSim(dumpFileName); |
180 |
|
|
181 |
< |
//parse md file and set up the system |
182 |
< |
SimCreator creator; |
183 |
< |
std::cout << "dumpFile = " << dumpFileName << "\n"; |
184 |
< |
SimInfo* info = creator.createSim(dumpFileName); |
185 |
< |
|
186 |
< |
RealType maxLen; |
187 |
< |
RealType zmaxLen; |
188 |
< |
if (args_info.length_given) { |
189 |
< |
maxLen = args_info.length_arg; |
190 |
< |
if (args_info.zlength_given){ |
191 |
< |
zmaxLen = args_info.zlength_arg; |
192 |
< |
} |
181 |
> |
RealType maxLen; |
182 |
> |
RealType zmaxLen; |
183 |
> |
if (args_info.length_given) { |
184 |
> |
maxLen = args_info.length_arg; |
185 |
> |
if (args_info.zlength_given){ |
186 |
> |
zmaxLen = args_info.zlength_arg; |
187 |
> |
} |
188 |
> |
} else { |
189 |
> |
Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
190 |
> |
maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; |
191 |
> |
zmaxLen = hmat(2,2); |
192 |
> |
} |
193 |
> |
|
194 |
> |
StaticAnalyser* analyser; |
195 |
> |
if (args_info.gofr_given){ |
196 |
> |
analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, |
197 |
> |
args_info.nbins_arg); |
198 |
> |
} else if (args_info.gofz_given) { |
199 |
> |
analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen, |
200 |
> |
args_info.nbins_arg); |
201 |
> |
} else if (args_info.r_z_given) { |
202 |
> |
analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen, |
203 |
> |
args_info.nbins_arg, args_info.nbins_z_arg); |
204 |
> |
} else if (args_info.r_theta_given) { |
205 |
> |
analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, |
206 |
> |
args_info.nbins_arg, args_info.nanglebins_arg); |
207 |
> |
} else if (args_info.r_omega_given) { |
208 |
> |
analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, |
209 |
> |
args_info.nbins_arg, args_info.nanglebins_arg); |
210 |
> |
} else if (args_info.theta_omega_given) { |
211 |
> |
analyser = new GofAngle2(info, dumpFileName, sele1, sele2, |
212 |
> |
args_info.nanglebins_arg); |
213 |
> |
} else if (args_info.gxyz_given) { |
214 |
> |
if (args_info.refsele_given) { |
215 |
> |
analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, |
216 |
> |
maxLen, args_info.nbins_arg); |
217 |
|
} else { |
218 |
< |
Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
219 |
< |
maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; |
220 |
< |
zmaxLen = hmat(2,2); |
218 |
> |
sprintf( painCave.errMsg, |
219 |
> |
"--refsele must set when --gxyz is used"); |
220 |
> |
painCave.severity = OPENMD_ERROR; |
221 |
> |
painCave.isFatal = 1; |
222 |
> |
simError(); |
223 |
> |
} |
224 |
> |
} else if (args_info.twodgofr_given){ |
225 |
> |
if (args_info.dz_given) { |
226 |
> |
analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen, |
227 |
> |
args_info.dz_arg, args_info.nbins_arg); |
228 |
> |
} else { |
229 |
> |
sprintf( painCave.errMsg, |
230 |
> |
"A slab width (dz) must be specified when calculating TwoDGofR"); |
231 |
> |
painCave.severity = OPENMD_ERROR; |
232 |
> |
painCave.isFatal = 1; |
233 |
> |
simError(); |
234 |
|
} |
235 |
< |
|
236 |
< |
StaticAnalyser* analyser; |
237 |
< |
if (args_info.gofr_given){ |
238 |
< |
analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, |
239 |
< |
args_info.nbins_arg); |
240 |
< |
} else if (args_info.gofz_given) { |
241 |
< |
analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen, |
242 |
< |
args_info.nbins_arg); |
243 |
< |
} else if (args_info.r_z_given) { |
244 |
< |
analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen, |
245 |
< |
args_info.nbins_arg, args_info.nbins_z_arg); |
246 |
< |
} else if (args_info.r_theta_given) { |
247 |
< |
analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, |
248 |
< |
args_info.nbins_arg, args_info.nanglebins_arg); |
249 |
< |
} else if (args_info.r_omega_given) { |
250 |
< |
analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, |
251 |
< |
args_info.nbins_arg, args_info.nanglebins_arg); |
252 |
< |
} else if (args_info.theta_omega_given) { |
253 |
< |
analyser = new GofAngle2(info, dumpFileName, sele1, sele2, |
254 |
< |
args_info.nanglebins_arg); |
255 |
< |
} else if (args_info.gxyz_given) { |
256 |
< |
if (args_info.refsele_given) { |
257 |
< |
analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, |
258 |
< |
maxLen, args_info.nbins_arg); |
259 |
< |
} else { |
260 |
< |
sprintf( painCave.errMsg, |
261 |
< |
"--refsele must set when --gxyz is used"); |
262 |
< |
painCave.severity = OPENMD_ERROR; |
263 |
< |
painCave.isFatal = 1; |
264 |
< |
simError(); |
265 |
< |
} |
266 |
< |
} else if (args_info.p2_given) { |
267 |
< |
analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
268 |
< |
} else if (args_info.rp2_given){ |
269 |
< |
analyser = new RippleOP(info, dumpFileName, sele1, sele2); |
270 |
< |
} else if (args_info.bo_given){ |
271 |
< |
if (args_info.rcut_given) { |
272 |
< |
analyser = new BondOrderParameter(info, dumpFileName, sele1, |
273 |
< |
args_info.rcut_arg, |
274 |
< |
args_info.nbins_arg); |
275 |
< |
} else { |
276 |
< |
sprintf( painCave.errMsg, |
277 |
< |
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
278 |
< |
painCave.severity = OPENMD_ERROR; |
279 |
< |
painCave.isFatal = 1; |
280 |
< |
simError(); |
281 |
< |
} |
282 |
< |
} else if (args_info.bor_given){ |
283 |
< |
if (args_info.rcut_given) { |
284 |
< |
analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg, |
285 |
< |
args_info.nbins_arg, maxLen); |
286 |
< |
} else { |
287 |
< |
sprintf( painCave.errMsg, |
288 |
< |
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
289 |
< |
painCave.severity = OPENMD_ERROR; |
290 |
< |
painCave.isFatal = 1; |
291 |
< |
simError(); |
292 |
< |
} |
293 |
< |
} else if (args_info.bad_given){ |
294 |
< |
if (args_info.rcut_given) { |
295 |
< |
analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg, |
296 |
< |
args_info.nbins_arg); |
297 |
< |
} else { |
298 |
< |
sprintf( painCave.errMsg, |
299 |
< |
"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions"); |
300 |
< |
painCave.severity = OPENMD_ERROR; |
301 |
< |
painCave.isFatal = 1; |
302 |
< |
simError(); |
303 |
< |
} |
304 |
< |
} else if (args_info.scd_given) { |
305 |
< |
if (batchMode) { |
306 |
< |
analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg, |
307 |
< |
args_info.begin_arg, args_info.end_arg); |
308 |
< |
} else{ |
309 |
< |
std::string sele3 = args_info.sele3_arg; |
310 |
< |
analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3); |
311 |
< |
} |
312 |
< |
}else if (args_info.density_given) { |
313 |
< |
analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, |
314 |
< |
args_info.nbins_arg); |
315 |
< |
} else if (args_info.slab_density_given) { |
316 |
< |
analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg); |
317 |
< |
} else if (args_info.p_angle_given) { |
318 |
< |
analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg); |
235 |
> |
} else if (args_info.p2_given) { |
236 |
> |
if (args_info.sele1_given) { |
237 |
> |
if (args_info.sele2_given) |
238 |
> |
analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
239 |
> |
else |
240 |
> |
analyser = new P2OrderParameter(info, dumpFileName, sele1); |
241 |
> |
} else { |
242 |
> |
sprintf( painCave.errMsg, |
243 |
> |
"At least one selection script (--sele1) must be specified when calculating P2 order parameters"); |
244 |
> |
painCave.severity = OPENMD_ERROR; |
245 |
> |
painCave.isFatal = 1; |
246 |
> |
simError(); |
247 |
> |
} |
248 |
> |
} else if (args_info.rp2_given){ |
249 |
> |
analyser = new RippleOP(info, dumpFileName, sele1, sele2); |
250 |
> |
} else if (args_info.bo_given){ |
251 |
> |
if (args_info.rcut_given) { |
252 |
> |
analyser = new BondOrderParameter(info, dumpFileName, sele1, |
253 |
> |
args_info.rcut_arg, |
254 |
> |
args_info.nbins_arg); |
255 |
> |
} else { |
256 |
> |
sprintf( painCave.errMsg, |
257 |
> |
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
258 |
> |
painCave.severity = OPENMD_ERROR; |
259 |
> |
painCave.isFatal = 1; |
260 |
> |
simError(); |
261 |
> |
} |
262 |
> |
|
263 |
> |
} else if (args_info.tet_param_given) { |
264 |
> |
if (args_info.rcut_given) { |
265 |
> |
analyser = new TetrahedralityParam(info, dumpFileName, sele1, |
266 |
> |
args_info.rcut_arg, |
267 |
> |
args_info.nbins_arg); |
268 |
> |
} else { |
269 |
> |
sprintf( painCave.errMsg, |
270 |
> |
"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters"); |
271 |
> |
painCave.severity = OPENMD_ERROR; |
272 |
> |
painCave.isFatal = 1; |
273 |
> |
simError(); |
274 |
> |
} |
275 |
> |
} else if (args_info.tet_param_z_given) { |
276 |
> |
if (args_info.rcut_given) { |
277 |
> |
analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, |
278 |
> |
args_info.rcut_arg, |
279 |
> |
args_info.nbins_arg); |
280 |
> |
} else { |
281 |
> |
sprintf( painCave.errMsg, |
282 |
> |
"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters"); |
283 |
> |
painCave.severity = OPENMD_ERROR; |
284 |
> |
painCave.isFatal = 1; |
285 |
> |
simError(); |
286 |
> |
} |
287 |
> |
} else if (args_info.bor_given){ |
288 |
> |
if (args_info.rcut_given) { |
289 |
> |
analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg, |
290 |
> |
args_info.nbins_arg, maxLen); |
291 |
> |
} else { |
292 |
> |
sprintf( painCave.errMsg, |
293 |
> |
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
294 |
> |
painCave.severity = OPENMD_ERROR; |
295 |
> |
painCave.isFatal = 1; |
296 |
> |
simError(); |
297 |
> |
} |
298 |
> |
} else if (args_info.bad_given){ |
299 |
> |
if (args_info.rcut_given) { |
300 |
> |
analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg, |
301 |
> |
args_info.nbins_arg); |
302 |
> |
} else { |
303 |
> |
sprintf( painCave.errMsg, |
304 |
> |
"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions"); |
305 |
> |
painCave.severity = OPENMD_ERROR; |
306 |
> |
painCave.isFatal = 1; |
307 |
> |
simError(); |
308 |
> |
} |
309 |
> |
} else if (args_info.scd_given) { |
310 |
> |
if (batchMode) { |
311 |
> |
analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg, |
312 |
> |
args_info.begin_arg, args_info.end_arg); |
313 |
> |
} else{ |
314 |
> |
std::string sele3 = args_info.sele3_arg; |
315 |
> |
analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3); |
316 |
> |
} |
317 |
> |
}else if (args_info.density_given) { |
318 |
> |
analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, |
319 |
> |
args_info.nbins_arg); |
320 |
> |
} else if (args_info.count_given) { |
321 |
> |
analyser = new ObjectCount(info, dumpFileName, sele1 ); |
322 |
> |
} else if (args_info.slab_density_given) { |
323 |
> |
analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg); |
324 |
> |
} else if (args_info.p_angle_given) { |
325 |
> |
analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg); |
326 |
|
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
327 |
< |
}else if (args_info.hxy_given) { |
328 |
< |
analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, |
329 |
< |
args_info.nbins_y_arg, args_info.nbins_arg); |
327 |
> |
}else if (args_info.hxy_given) { |
328 |
> |
analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, |
329 |
> |
args_info.nbins_y_arg, args_info.nbins_arg); |
330 |
|
#endif |
331 |
< |
}else if (args_info.rho_r_given) { |
332 |
< |
if (args_info.radius_given){ |
333 |
< |
analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg); |
334 |
< |
}else{ |
335 |
< |
sprintf( painCave.errMsg, |
336 |
< |
"A particle radius (radius) must be specified when calculating Rho(r)"); |
337 |
< |
painCave.severity = OPENMD_ERROR; |
338 |
< |
painCave.isFatal = 1; |
339 |
< |
simError(); |
286 |
< |
} |
287 |
< |
}else if (args_info.hullvol_given) { |
288 |
< |
analyser = new NanoVolume(info, dumpFileName, sele1); |
331 |
> |
}else if (args_info.rho_r_given) { |
332 |
> |
if (args_info.radius_given){ |
333 |
> |
analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg); |
334 |
> |
}else{ |
335 |
> |
sprintf( painCave.errMsg, |
336 |
> |
"A particle radius (radius) must be specified when calculating Rho(r)"); |
337 |
> |
painCave.severity = OPENMD_ERROR; |
338 |
> |
painCave.isFatal = 1; |
339 |
> |
simError(); |
340 |
|
} |
341 |
+ |
} else if (args_info.hullvol_given) { |
342 |
+ |
analyser = new NanoVolume(info, dumpFileName, sele1); |
343 |
+ |
} else if (args_info.rodlength_given) { |
344 |
+ |
analyser = new NanoLength(info, dumpFileName, sele1); |
345 |
+ |
} else if (args_info.angle_r_given) { |
346 |
+ |
analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg); |
347 |
+ |
} |
348 |
+ |
|
349 |
+ |
if (args_info.output_given) { |
350 |
+ |
analyser->setOutputName(args_info.output_arg); |
351 |
+ |
} |
352 |
+ |
if (args_info.step_given) { |
353 |
+ |
analyser->setStep(args_info.step_arg); |
354 |
+ |
} |
355 |
+ |
|
356 |
+ |
analyser->process(); |
357 |
|
|
358 |
< |
if (args_info.output_given) { |
359 |
< |
analyser->setOutputName(args_info.output_arg); |
293 |
< |
} |
294 |
< |
if (args_info.step_given) { |
295 |
< |
analyser->setStep(args_info.step_arg); |
296 |
< |
} |
358 |
> |
delete analyser; |
359 |
> |
delete info; |
360 |
|
|
361 |
< |
analyser->process(); |
299 |
< |
|
300 |
< |
delete analyser; |
301 |
< |
delete info; |
302 |
< |
|
303 |
< |
return 0; |
361 |
> |
return 0; |
362 |
|
} |
363 |
|
|