--- trunk/src/applications/staticProps/StaticProps.cpp 2008/01/23 22:01:34 1222 +++ trunk/src/applications/staticProps/StaticProps.cpp 2009/11/25 20:02:06 1390 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,15 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). */ #include @@ -70,7 +70,7 @@ #endif #include "applications/staticProps/RhoR.hpp" -using namespace oopse; +using namespace OpenMD; int main(int argc, char* argv[]){ @@ -97,7 +97,7 @@ int main(int argc, char* argv[]){ if (args_info.sele1_given) { sele1 = args_info.sele1_arg; } else { - char* sele1Env= getenv("OOPSE_SELE1"); + char* sele1Env= getenv("SELECTION1"); if (sele1Env) { sele1 = sele1Env; } else { @@ -111,7 +111,7 @@ int main(int argc, char* argv[]){ if (args_info.sele2_given) { sele2 = args_info.sele2_arg; } else { - char* sele2Env = getenv("OOPSE_SELE2"); + char* sele2Env = getenv("SELECTION1"); if (sele2Env) { sele2 = sele2Env; } else { @@ -123,8 +123,8 @@ int main(int argc, char* argv[]){ // Problems if sele1 wasn't specified, but // if (!args_info.scd_given) { // sprintf( painCave.errMsg, -// "neither --sele1 option nor $OOPSE_SELE1 is set"); -// painCave.severity = OOPSE_ERROR; +// "neither --sele1 option nor $SELECTION1 is set"); +// painCave.severity = OPENMD_ERROR; // painCave.isFatal = 1; // simError(); // } @@ -134,8 +134,8 @@ int main(int argc, char* argv[]){ // if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) { // sprintf( painCave.errMsg, -// "neither --sele2 option nor $OOPSE_SELE2 is set"); -// painCave.severity = OOPSE_ERROR; +// "neither --sele2 option nor $SELECTION1 is set"); +// painCave.severity = OPENMD_ERROR; // painCave.isFatal = 1; // simError(); // } @@ -150,7 +150,7 @@ int main(int argc, char* argv[]){ sprintf( painCave.errMsg, "below conditions are not satisfied:\n" "0 <= begin && 0<= end && begin <= end-2\n"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } @@ -159,7 +159,7 @@ int main(int argc, char* argv[]){ sprintf( painCave.errMsg, "either --sele1, --sele2, --sele3 are specified," " or --molname, --begin, --end are specified\n"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); @@ -184,7 +184,7 @@ int main(int argc, char* argv[]){ analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nbins_arg); } else if (args_info.gofz_given) { - analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen, + analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen, args_info.nbins_arg); } else if (args_info.r_theta_given) { analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, @@ -202,7 +202,7 @@ int main(int argc, char* argv[]){ } else { sprintf( painCave.errMsg, "--refsele must set when --gxyz is used"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } @@ -218,7 +218,7 @@ int main(int argc, char* argv[]){ } else { sprintf( painCave.errMsg, "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } @@ -229,7 +229,7 @@ int main(int argc, char* argv[]){ } else { sprintf( painCave.errMsg, "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } @@ -240,7 +240,7 @@ int main(int argc, char* argv[]){ } else { sprintf( painCave.errMsg, "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } @@ -253,11 +253,10 @@ int main(int argc, char* argv[]){ analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3); } }else if (args_info.density_given) { - analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, + analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, args_info.nbins_arg); } else if (args_info.slab_density_given) { - Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); - analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg); + analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg); #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) }else if (args_info.hxy_given) { analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, @@ -269,7 +268,7 @@ int main(int argc, char* argv[]){ }else{ sprintf( painCave.errMsg, "A particle radius (radius) must be specified when calculating Rho(r)"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); }