Added the ability to wrap input in period (#115)

pelahi · Jan 4, 2024 · 9902dfb · 9902dfb
1 parent 01ad988
commit 9902dfb
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Showing 3 changed files with 16 additions and 0 deletions.
diff --git a/doc/getting.rst b/doc/getting.rst
@@ -94,6 +94,10 @@ These can be passed to ``cmake``
             | ``VR_ADIOS``: boolean on whether to include ADIOS support
             | ``ADIOS_DIR``: specify a local directory containing ADIOS library.
 
+    * Enable variation in input
+        * to allow particles in input to be outside the periodic bounds
+            | ``VR_PARTICLES_OUTSIDE_PERIOD_LIMIT``: boolean to allow particles to be outside periodic limit and be wrapped into periodic volume. Enable this only if you are certain that particles can be outside volume. Otherwise, error report by VR might indicate incorrect reading of the input. 
+
     * To set directories of required libraries
         * Set the directories of the following libraries
             | ``GSL_DIR =``

diff --git a/src/hdfio.cxx b/src/hdfio.cxx
@@ -2997,6 +2997,9 @@ void ReadHDF(Options &opt, vector<Particle> &Part, const Int_t nbodies,Particle
                     }
                 LOG(debug) << "Now getting where the data should be sent";
                 for (unsigned long long nn=0;nn<nchunk;nn++) {
+#ifdef PERIODWRAPINPUT
+                    PeriodWrapInput<double>(hdf_header_info[i].BoxSize, doublebuff[nn*3],doublebuff[nn*3+1],doublebuff[nn*3+2]);
+#endif
                     ibuf=MPIGetParticlesProcessor(opt, doublebuff[nn*3],doublebuff[nn*3+1],doublebuff[nn*3+2]);
                     ibufindex=ibuf*BufSize+Nbuf[ibuf];
                     //reset hydro quantities of buffer
@@ -3401,6 +3404,9 @@ void ReadHDF(Options &opt, vector<Particle> &Part, const Int_t nbodies,Particle
 #endif
 #endif
                     for (int nn=0;nn<nchunk;nn++) {
+#ifdef PERIODWRAPINPUT
+                    PeriodWrapInput<double>(hdf_header_info[i].BoxSize, doublebuff[nn*3],doublebuff[nn*3+1],doublebuff[nn*3+2]);
+#endif
                     ibuf=MPIGetParticlesProcessor(opt, doublebuff[nn*3],doublebuff[nn*3+1],doublebuff[nn*3+2]);
                     ibufindex=ibuf*BufSize+Nbuf[ibuf];
                     //reset hydro quantities of buffer

diff --git a/src/mpihdfio.cxx b/src/mpihdfio.cxx
@@ -237,6 +237,9 @@ void MPINumInDomainHDF(Options &opt)
                     //setup hyperslab so that it is loaded into the buffer
                     HDF5ReadHyperSlabReal(doublebuff,partsdataset[i*NHDFTYPE+k], partsdataspace[i*NHDFTYPE+k], 1, 3, nchunk, n, plist_id);
                     for (auto nn=0;nn<nchunk;nn++) {
+#ifdef PERIODWRAPINPUT
+                    PeriodWrapInput<double>(hdf_header_info[i].BoxSize, doublebuff[nn*3],doublebuff[nn*3+1],doublebuff[nn*3+2]);
+#endif
                         ibuf=MPIGetParticlesProcessor(opt, doublebuff[nn*3],doublebuff[nn*3+1],doublebuff[nn*3+2]);
                         Nbuf[ibuf]++;
                     }
@@ -263,6 +266,9 @@ void MPINumInDomainHDF(Options &opt)
                         HDF5ReadHyperSlabReal(doublebuff, partsdataset[i*NHDFTYPE+k], partsdataspace[i*NHDFTYPE+k], 1, 3, nchunk, n, plist_id);
 
                         for (auto nn=0;nn<nchunk;nn++) {
+#ifdef PERIODWRAPINPUT
+                    PeriodWrapInput<double>(hdf_header_info[i].BoxSize, doublebuff[nn*3],doublebuff[nn*3+1],doublebuff[nn*3+2]);
+#endif
                             ibuf=MPIGetParticlesProcessor(opt, doublebuff[nn*3],doublebuff[nn*3+1],doublebuff[nn*3+2]);
                             Nbaryonbuf[ibuf]++;
                         }