Amber-MD · drroe · Dec 6, 2022 · Sep 1, 2022 · Sep 1, 2022 · Sep 1, 2022
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
@@ -2911,7 +2911,7 @@ status open
 \begin_layout Plain Layout
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="20" columns="5">
+<lyxtabular version="3" rows="21" columns="5">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="20text%">
 <column alignment="center" valignment="top" width="20text%">
@@ -3822,7 +3822,7 @@ Used for cluster analysis.
 </cell>
 </row>
 <row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -3831,7 +3831,7 @@ Pairwise Cache (NetCDF)
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -3840,7 +3840,7 @@ Pairwise Cache (NetCDF)
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -3849,7 +3849,7 @@ nccmatrix
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -3858,13 +3858,60 @@ pairwise distances
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
 Used for cluster analysis.
 \end_layout
 
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+NetCDF Data
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+.nc
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+netcdf
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+All data
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Only state info saved for pH data.
+\end_layout
+
 \end_inset
 </cell>
 </row>

diff --git a/src/Action_Bounds.cpp b/src/Action_Bounds.cpp
@@ -8,6 +8,7 @@
 Action_Bounds::Action_Bounds() :
   outfile_(0),
   offset_(1),
+  gridIsSetup_(false),
   grid_(0),
   ds_xmin_(0),
   ds_ymin_(0),
@@ -44,6 +45,7 @@ Action::RetType Action_Bounds::Init(ArgList& actionArgs, ActionInit& init, int d
   if (mask_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
   std::string dsname = actionArgs.GetStringKey("name");
   offset_ = actionArgs.getKeyInt("offset", 1);
+  gridIsSetup_ = false;
   if (dxyz_[0] > -1.0) {
     // Set up grid
     if (dsname.empty()) {
@@ -127,14 +129,42 @@ int Action_Bounds::SyncAction() {
   trajComm_.ReduceMaster( &buf, max_, 3, MPI_DOUBLE, MPI_MAX );
   if (trajComm_.Master())
     std::copy( buf, buf+3, max_ );
+  // Set up the grid here so all processes have it.
+  trajComm_.MasterBcast(min_, 3, MPI_DOUBLE);
+  trajComm_.MasterBcast(max_, 3, MPI_DOUBLE);
+  calc_center_and_bins();
   return 0;
 }
 #endif
 
+/** Calculate bounds center and grid bins based on min/max/spacing. */
+int Action_Bounds::calc_center_and_bins() {
+  if (gridIsSetup_) return 0;
+  for (int i = 0; i < 3; i++) {
+    if (dxyz_[i] > 0.0) {
+      center_[i] = (max_[i] + min_[i]) / 2.0;
+      long int nbins = (long int)ceil( (max_[i] - min_[i]) / dxyz_[i] ) + (long int)offset_;
+      if (nbins < 0) {
+        mprinterr("Error: Overflow in bounds dim %i: max=%f min=%f spacing=%f\n",
+                  i, max_[i], min_[i], dxyz_[i]);
+        return 1;
+      }
+      nxyz_[i] = (size_t)nbins;
+    }
+  }
+  if (grid_ != 0) {
+    DataSet_3D& grid3d = static_cast<DataSet_3D&>( *grid_ );
+    if (grid3d.Allocate_N_C_D( nxyz_[0], nxyz_[1], nxyz_[2], center_, dxyz_ )) {
+      mprinterr("Error: Could not allocate grid %s\n", grid_->legend());
+      return 1;
+    }
+  }
+  gridIsSetup_ = true;
+  return 0;
+} 
+
 void Action_Bounds::Print() {
   static const char cXYZ[3] = {'X', 'Y', 'Z'};
-  Vec3 center;
-  size_t nxyz[3];
 
   mprintf("    BOUNDS: Output to %s\n", outfile_->Filename().full());
   ds_xmin_->Add(0, min_  );
@@ -143,19 +173,14 @@ void Action_Bounds::Print() {
   ds_xmax_->Add(0, max_  );
   ds_ymax_->Add(0, max_+1);
   ds_zmax_->Add(0, max_+2);
+
+  calc_center_and_bins();
+
   for (int i = 0; i < 3; i++) {
     outfile_->Printf("%f < %c < %f", min_[i], cXYZ[i], max_[i]);
-    if (dxyz_[i] > 0.0) {
-      center[i] = (max_[i] + min_[i]) / 2.0;
-      long int nbins = (long int)ceil( (max_[i] - min_[i]) / dxyz_[i] ) + (long int)offset_;
-      nxyz[i] = (size_t)nbins;
-      outfile_->Printf("\tCenter= %f  Bins=%zu", center[i], nxyz[i]);
-    }
+    if (dxyz_[i] > 0.0)
+      outfile_->Printf("\tCenter= %f  Bins=%zu", center_[i], nxyz_[i]);
     outfile_->Printf("\n");
   }
-  if (grid_ != 0) {
-    DataSet_3D& grid3d = static_cast<DataSet_3D&>( *grid_ );
-    if (grid3d.Allocate_N_C_D( nxyz[0], nxyz[1], nxyz[2], center, dxyz_ ))
-      mprinterr("Error: Could not allocate grid %s\n", grid_->legend());
-  }
+
 }
diff --git a/src/Action_Bounds.h b/src/Action_Bounds.h
@@ -1,6 +1,7 @@
 #ifndef INC_ACTION_BOUNDS_H
 #define INC_ACTION_BOUNDS_H
 #include "Action.h"
+#include <cstddef> // size_t
 /// Report the min/max XYZ values for atoms in mask.
 class Action_Bounds : public Action {
   public:
@@ -16,13 +17,19 @@ class Action_Bounds : public Action {
     Parallel::Comm trajComm_;
 #   endif
     void Print();
-    AtomMask mask_;
-    CpptrajFile* outfile_;
-    double max_[3];
-    double min_[3];
-    Vec3 dxyz_;
-    int offset_;
-    DataSet* grid_;
+
+    int calc_center_and_bins();
+
+    AtomMask mask_;        ///< Mask of atoms to obtain the bounds of.
+    CpptrajFile* outfile_; ///< File to print bounds to.
+    double max_[3];        ///< Minimum extent of any atom in mask.
+    double min_[3];        ///< Maximum extent of any atom in mask.
+    Vec3 dxyz_;            ///< Grid spacing (if creating a grid from bounds).
+    size_t nxyz_[3];       ///< # grid bins in each dimension based on spacing.
+    Vec3 center_;          ///< Grid center based on min/max.
+    int offset_;           ///< # bins offset for grid.
+    bool gridIsSetup_;     ///< True if grid has already been set up for bounds.
+    DataSet* grid_;        ///< Hold grid created from bounds.
     DataSet* ds_xmin_;
     DataSet* ds_ymin_;
     DataSet* ds_zmin_;

diff --git a/src/Cluster/Cframes.h b/src/Cluster/Cframes.h
@@ -28,6 +28,7 @@ class Cframes {
     void clear()                           { frames_.clear();        }
     void reserve(std::size_t n)            { frames_.reserve(n);     }
     Iarray const& Data()             const { return frames_;         }
+    int* Ptr()                             { return &frames_[0];     }
     bool empty()                     const { return frames_.empty(); }
 
     bool HasFrame(int) const;

diff --git a/src/Cluster/Cmatrix_NC.cpp b/src/Cluster/Cmatrix_NC.cpp
@@ -29,7 +29,7 @@ Cpptraj::Cluster::Cmatrix_NC::~Cmatrix_NC() {
 
 /** \return true if NetCDF file has CPPTRAJ_CMATRIX conventions. */
 bool Cpptraj::Cluster::Cmatrix_NC::IsCpptrajCmatrix(int NCID) {
-  return (NC::GetAttrText(NCID, "Conventions") == "CPPTRAJ_CMATRIX");
+  return (NC::GetConventions(NCID) == NC::NC_CPPTRAJCMATRIX);
 }
 
 #else /* BINTRAJ */
@@ -251,7 +251,7 @@ int Cpptraj::Cluster::Cmatrix_NC::CreateCmatrix(FileName const& fname, unsigned
     actualFrames_VID_ = -1;
 
   // Attributes
-  if (NC::CheckErr(nc_put_att_text(ncid_, NC_GLOBAL, "Conventions", 15, "CPPTRAJ_CMATRIX")))
+  if (NC::PutConventions(ncid_, NC::NC_CPPTRAJCMATRIX))
     return 1;
   if (NC::CheckErr(nc_put_att_text(ncid_, NC_GLOBAL, "Version", 3, "1.0")))
     return 1;

diff --git a/src/DataFile.cpp b/src/DataFile.cpp
@@ -29,6 +29,7 @@
 #include "DataIO_Cmatrix_Binary.h"
 #include "DataIO_Cmatrix_NC.h"
 #include "DataIO_Peaks.h"
+#include "DataIO_NetCDF.h"
 #include "DataIO_AmberEne.h"
 
 // CONSTRUCTOR
@@ -76,10 +77,16 @@ const FileTypes::AllocToken DataFile::DF_AllocArray[] = {
   { "Pairwise Cache (NetCDF)", 0,                        0,          0 },
 # endif
   { "Peaks",              0,                             0,            DataIO_Peaks::Alloc },
+# ifdef BINTRAJ
+  { "NetCDF data",             0,                        0,          DataIO_NetCDF::Alloc },
+# else
+  { "NetCDF data",             0,                        0,          0 },
+# endif
   { "Amber Energy File",  0,                             0,            DataIO_AmberEne::Alloc},
   { "Unknown Data file",  0,                       0,                        0                    }
 };
 
+/** Types that support reads. */
 const FileTypes::KeyToken DataFile::DF_KeyArray[] = {
   { DATAFILE,     "dat",    ".dat"   },
   { XMGRACE,      "grace",  ".agr"   },
@@ -96,6 +103,7 @@ const FileTypes::KeyToken DataFile::DF_KeyArray[] = {
   { CHARMMREPD,   "charmmrepd",   ".exch" },
   { CHARMMOUT,    "charmmout",    ".charmmout"},
   { CHARMMRTFPRM, "charmmrtfprm", ".rtfprm"},
+  { NETCDFDATA,   "netcdf",       ".nc" },
   { CMATRIX_BINARY,"cmatrix",     ".cmatrix" },
   { CMATRIX_NETCDF,"nccmatrix",   ".nccmatrix" },
   { PEAKS,        "peaks",        ".peaks" },
@@ -120,6 +128,7 @@ const FileTypes::KeyToken DataFile::DF_WriteKeyArray[] = {
   { CMATRIX_NETCDF,"nccmatrix", ".nccmatrix" },
   { CHARMMRTFPRM, "charmmrtfprm", ".prm" },
   { PEAKS,        "peaks",  ".peaks" },
+  { NETCDFDATA,   "netcdf", ".nc" },
   { UNKNOWN_DATA, 0,        0        }
 };
 
@@ -333,13 +342,15 @@ int DataFile::AddDataSet(DataSet* dataIn) {
               dataIn->legend());
     }
   } else {
-    if ((int)dataIn->Ndim() != dimension_) {
-      mprinterr("Error: DataSets in DataFile %s have dimension %i\n" 
-                "Error: Attempting to add set %s of dimension %zu\n", 
-                filename_.base(), dimension_,
-                dataIn->legend(), dataIn->Ndim());
-      return Error("Error: Adding DataSets with different dimensions to same file"
-                   " is currently unsupported.\n");
+    if (Type() != NETCDFDATA) {
+      if ((int)dataIn->Ndim() != dimension_) {
+        mprinterr("Error: DataSets in DataFile %s have dimension %i\n" 
+                  "Error: Attempting to add set %s of dimension %zu\n", 
+                  filename_.base(), dimension_,
+                  dataIn->legend(), dataIn->Ndim());
+        return Error("Error: Adding DataSets with different dimensions to same file"
+                     " is currently unsupported.\n");
+      }
     }
     if (!dataio_->CheckValidFor(*dataIn)) {
       mprinterr("Error: DataSet '%s' is not valid for DataFile '%s' format.\n",
@@ -501,7 +512,7 @@ int DataFile::WriteSetsToFile(FileName const& fname, DataSetList& setsToWrite)
             dftimer.Total());
 #   endif
     if (err > 0) 
-      mprinterr("Error writing %iD Data to %s\n", dimension_, fname.base());
+      mprinterr("Error: Could not write data sets to %s\n", fname.base());
   }
   return err;
 }

diff --git a/src/DataFile.h b/src/DataFile.h
@@ -18,7 +18,7 @@ class DataFile {
       DATAFILE=0, XMGRACE, GNUPLOT, XPLOR, OPENDX, REMLOG, MDOUT, EVECS,
       VECTRAJ, XVG, CCP4, CHARMMREPD, CHARMMFASTREP,
       CHARMMOUT, CPOUT, CHARMMRTFPRM, CMATRIX_BINARY, CMATRIX_NETCDF, PEAKS,
-      AMBERENE,
+      NETCDFDATA, AMBERENE,
       UNKNOWN_DATA 
     };
     DataFile();