/*****************************************************************************
*
* Copyright (c) 2000 - 2018, Lawrence Livermore National Security, LLC
* Produced at the Lawrence Livermore National Laboratory
* LLNL-CODE-442911
* All rights reserved.
*
* This file is  part of VisIt. For  details, see https://visit.llnl.gov/.  The
* full copyright notice is contained in the file COPYRIGHT located at the root
* of the VisIt distribution or at http://www.llnl.gov/visit/copyright.html.
*
* Redistribution  and  use  in  source  and  binary  forms,  with  or  without
* modification, are permitted provided that the following conditions are met:
*
*  - Redistributions of  source code must  retain the above  copyright notice,
*    this list of conditions and the disclaimer below.
*  - Redistributions in binary form must reproduce the above copyright notice,
*    this  list of  conditions  and  the  disclaimer (as noted below)  in  the
*    documentation and/or other materials provided with the distribution.
*  - Neither the name of  the LLNS/LLNL nor the names of  its contributors may
*    be used to endorse or promote products derived from this software without
*    specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT  HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR  IMPLIED WARRANTIES, INCLUDING,  BUT NOT  LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND  FITNESS FOR A PARTICULAR  PURPOSE
* ARE  DISCLAIMED. IN  NO EVENT  SHALL LAWRENCE  LIVERMORE NATIONAL  SECURITY,
* LLC, THE  U.S.  DEPARTMENT OF  ENERGY  OR  CONTRIBUTORS BE  LIABLE  FOR  ANY
* DIRECT,  INDIRECT,   INCIDENTAL,   SPECIAL,   EXEMPLARY,  OR   CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT  LIMITED TO, PROCUREMENT OF  SUBSTITUTE GOODS OR
* SERVICES; LOSS OF  USE, DATA, OR PROFITS; OR  BUSINESS INTERRUPTION) HOWEVER
* CAUSED  AND  ON  ANY  THEORY  OF  LIABILITY,  WHETHER  IN  CONTRACT,  STRICT
* LIABILITY, OR TORT  (INCLUDING NEGLIGENCE OR OTHERWISE)  ARISING IN ANY  WAY
* OUT OF THE  USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
* DAMAGE.
*
*****************************************************************************/

// ************************************************************************* //
//                            avtLAMMPSFileFormat.C                           //
// ************************************************************************* //

#include <avtMTMDFileFormatInterface.h>
#include <avtLAMMPSFileFormat.h>
#include <ADIOSFileObject.h>

#include <vtkFloatArray.h>
#include <vtkPolyData.h>
#include <vtkCellArray.h>
#include <avtDatabaseMetaData.h>
#include <DBOptionsAttributes.h>
#include <Expression.h>
#include <InvalidVariableException.h>

#include <string>
using std::string;


// ****************************************************************************
//  Method: avtLAMMPSFileFormat::Identify
//
//  Purpose:
//      Determine if this file is of this flavor.
//
//  Programmer: Dave Pugmire
//  Creation:   Wed Oct 29 14:12:25 PST 2014
//
// ****************************************************************************

bool
avtLAMMPSFileFormat::Identify(const char *fname)
{
    ADIOSFileObject *f = new ADIOSFileObject(fname);
    f->Open();

    std::map<std::string, ADIOS_VARINFO*>::const_iterator si;
    int scalarCount = 0;
    for (si = f->scalars.begin(); si != f->scalars.end(); si++)
    {
        if (si->first.find("boxxlo") != string::npos) scalarCount++;
        else if (si->first.find("boxxhi") != string::npos) scalarCount++;
        else if (si->first.find("boxylo") != string::npos) scalarCount++;
        else if (si->first.find("boxyhi") != string::npos) scalarCount++;
        else if (si->first.find("boxzlo") != string::npos) scalarCount++;
        else if (si->first.find("boxzhi") != string::npos) scalarCount++;
        else if (si->first.find("natoms") != string::npos) scalarCount++;
    }
    delete f;
    
    return (scalarCount == 7);
}


// ****************************************************************************
//  Method: avtLAMMPSFileFormat::CreateInterface
//
//  Purpose:
//      Create an interface for this reader.
//
//  Programmer: Dave Pugmire
//  Creation:   Wed Oct 29 14:12:25 PST 2014
//
// ****************************************************************************

avtFileFormatInterface *
avtLAMMPSFileFormat::CreateInterface(const char *const *list,
                                  int nList,
                                  int nBlock)
{
    int nTimestepGroups = nList / nBlock;
    avtMTMDFileFormat **ffl = new avtMTMDFileFormat*[nTimestepGroups];
    for (int i = 0 ; i < nTimestepGroups ; i++)
        ffl[i] = new avtLAMMPSFileFormat(list[i*nBlock]);
    
    return new avtMTMDFileFormatInterface(ffl, nTimestepGroups);
}


// ****************************************************************************
//  Method: avtLAMMPSFileFormat constructor
//
//  Programmer: pugmire -- generated by xml2avt
//  Creation:   Wed Oct 29 14:12:25 PST 2014
//
// ****************************************************************************

avtLAMMPSFileFormat::avtLAMMPSFileFormat(const char *filename)
    : avtMTMDFileFormat(filename)
{
    file = new ADIOSFileObject(filename);
}


// ****************************************************************************
//  Method: avtEMSTDFileFormat::GetNTimesteps
//
//  Purpose:
//      Tells the rest of the code how many timesteps there are in this file.
//
//  Programmer: pugmire -- generated by xml2avt
//  Creation:   Wed Oct 29 14:12:25 PST 2014
//
// ****************************************************************************

int
avtLAMMPSFileFormat::GetNTimesteps(void)
{
    return file->NumTimeSteps();
}


// ****************************************************************************
//  Method: avtLAMMPSFileFormat::FreeUpResources
//
//  Purpose:
//      When VisIt is done focusing on a particular timestep, it asks that
//      timestep to free up any resources (memory, file descriptors) that
//      it has associated with it.  This method is the mechanism for doing
//      that.
//
//  Programmer: pugmire -- generated by xml2avt
//  Creation:   Wed Oct 29 14:12:25 PST 2014
//
// ****************************************************************************

void
avtLAMMPSFileFormat::FreeUpResources(void)
{
}


// ****************************************************************************
//  Method: avtLAMMPSFileFormat::PopulateDatabaseMetaData
//
//  Purpose:
//      This database meta-data object is like a table of contents for the
//      file.  By populating it, you are telling the rest of VisIt what
//      information it can request from you.
//
//  Programmer: pugmire -- generated by xml2avt
//  Creation:   Wed Oct 29 14:12:25 PST 2014
//
// ****************************************************************************

void
avtLAMMPSFileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData *md, int timeState)
{
    file->Open();

    avtMeshMetaData *mmd = new avtMeshMetaData("mesh", 1, 0,0,0,
                                               3, 1,
                                               AVT_POINT_MESH);
    md->Add(mmd);
    
    AddScalarVarToMetaData(md, "species", "mesh", AVT_NODECENT);
    AddScalarVarToMetaData(md, "id", "mesh", AVT_NODECENT);
}


// ****************************************************************************
//  Method: avtLAMMPSFileFormat::GetMesh
//
//  Purpose:
//      Gets the mesh associated with this file.  The mesh is returned as a
//      derived type of vtkDataSet (ie vtkRectilinearGrid, vtkStructuredGrid,
//      vtkUnstructuredGrid, etc).
//
//  Arguments:
//      timestate   The index of the timestate.  If GetNTimesteps returned
//                  'N' time steps, this is guaranteed to be between 0 and N-1.
//      domain      The index of the domain.  If there are NDomains, this
//                  value is guaranteed to be between 0 and NDomains-1,
//                  regardless of block origin.
//      meshname    The name of the mesh of interest.  This can be ignored if
//                  there is only one mesh.
//
//  Programmer: pugmire -- generated by xml2avt
//  Creation:   Wed Oct 29 14:12:25 PST 2014
//
// ****************************************************************************

vtkDataSet *
avtLAMMPSFileFormat::GetMesh(int timestate, int domain, const char *meshname)
{
    vtkPolyData *pd  = vtkPolyData::New();
    vtkPoints *pts = vtkPoints::New();

    pd->SetPoints(pts);
    pts->Delete();

    vtkDataArray *ptData = NULL;
    file->ReadScalarData("atoms", timestate, &ptData);
    int nPts = ptData->GetNumberOfTuples() / 5;

    pts->SetNumberOfPoints(nPts);
    double x, y, z;
    for (int i = 0; i < nPts; i++)
    {
        x = ptData->GetTuple1(i*5 + 2);
        y = ptData->GetTuple1(i*5 + 3);
        z = ptData->GetTuple1(i*5 + 4);
        pts->SetPoint(i, x,y,z);
    }
    ptData->Delete();

    vtkCellArray *verts = vtkCellArray::New();
    pd->SetVerts(verts);
    verts->Delete();
    
    for (int i = 0; i < nPts; i++)
    {
        verts->InsertNextCell(1);
        verts->InsertCellPoint(i);
    }

    return pd;
}


// ****************************************************************************
//  Method: avtLAMMPSFileFormat::GetVar
//
//  Purpose:
//      Gets a scalar variable associated with this file.  Although VTK has
//      support for many different types, the best bet is vtkFloatArray, since
//      that is supported everywhere through VisIt.
//
//  Arguments:
//      timestate  The index of the timestate.  If GetNTimesteps returned
//                 'N' time steps, this is guaranteed to be between 0 and N-1.
//      domain     The index of the domain.  If there are NDomains, this
//                 value is guaranteed to be between 0 and NDomains-1,
//                 regardless of block origin.
//      varname    The name of the variable requested.
//
//  Programmer: pugmire -- generated by xml2avt
//  Creation:   Wed Oct 29 14:12:25 PST 2014
//
// ****************************************************************************

vtkDataArray *
avtLAMMPSFileFormat::GetVar(int timestate, int domain, const char *varname)
{
    string vnm(varname);
    
    int offset = -1;
    if (vnm == "id")
        offset = 0;
    else if (vnm == "species")
        offset = 1;
    else
        EXCEPTION1(InvalidVariableException, varname);

    vtkDataArray *ptData = NULL;
    file->ReadScalarData("atoms", timestate, &ptData);
    int nPts = ptData->GetNumberOfTuples() / 5;

    vtkFloatArray *var = vtkFloatArray::New();
    var->SetNumberOfTuples(nPts);
    for (int i = 0; i < nPts; i++)
        var->SetTuple1(i, ptData->GetTuple1(i*5 + offset));
    
    ptData->Delete();
    
    return var;
}


// ****************************************************************************
//  Method: avtLAMMPSFileFormat::GetVectorVar
//
//  Purpose:
//      Gets a vector variable associated with this file.  Although VTK has
//      support for many different types, the best bet is vtkFloatArray, since
//      that is supported everywhere through VisIt.
//
//  Arguments:
//      timestate  The index of the timestate.  If GetNTimesteps returned
//                 'N' time steps, this is guaranteed to be between 0 and N-1.
//      domain     The index of the domain.  If there are NDomains, this
//                 value is guaranteed to be between 0 and NDomains-1,
//                 regardless of block origin.
//      varname    The name of the variable requested.
//
//  Programmer: pugmire -- generated by xml2avt
//  Creation:   Wed Oct 29 14:12:25 PST 2014
//
// ****************************************************************************

vtkDataArray *
avtLAMMPSFileFormat::GetVectorVar(int timestate, int domain,const char *varname)
{
    EXCEPTION1(InvalidVariableException, varname);
}
