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Fix Gaussian cube model and grid import.
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@trisyoungs
trisyoungs committed Oct 19, 2018
1 parent 839cb16 commit 8cd0981
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Showing 2 changed files with 70 additions and 109 deletions.
168 changes: 63 additions & 105 deletions src/plugins/io_cube/cube_funcs.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,13 +55,13 @@ PluginTypes::PluginType CubeGridPlugin::type() const
// Return category of plugin
int CubeGridPlugin::category() const
{
return PluginTypes::ModelFilePlugin;
return PluginTypes::GridFilePlugin;
}

// Name of plugin
QString CubeGridPlugin::name() const
{
return QString("Cube (dlputils) 3D probability density");
return QString("Gaussian cube");
}

// Nickname of plugin
Expand All @@ -79,7 +79,7 @@ bool CubeGridPlugin::enabled() const
// Description (long name) of plugin
QString CubeGridPlugin::description() const
{
return QString("Import/export for cube files");
return QString("Import for Gaussian cube files");
}

// Related file extensions
Expand Down Expand Up @@ -107,108 +107,66 @@ bool CubeGridPlugin::canImport() const
// Import data from the specified file
bool CubeGridPlugin::importData()
{
//filter(type="importmodel", name="Gaussian Cube", nickname="cube", extension="cube", glob="*.cube", zmap="numeric")
//{
// # Variable declaration
// string e,title;
// int natoms,nx,ny,nz,i,j,k;
// vector origin, x,y,z;
// double rx,ry,rz,data;
//
// # Since we must create the model first, and then set all grid date afterwards,
// # store all grid-related values for later until we've finalised the model.
//
// # Lines 1-2: Comments (use first as title)
// getLine(title);
// skipLine();
//
// # Line 3: Number of atoms and coordinate origin of surface
// readLine(natoms, origin.x, origin.y, origin.z);
//
// # Lines 4-6: Number of voxels and axis vector
// readLine(nx, x.x, x.y, x.z);
// readLine(ny, y.x, y.y, y.z);
// readLine(nz, z.x, z.y, z.z);
//
// # Lines 7-(7+natoms) Molecule Definition
// newModel(title);
// for (i=0; i<natoms; ++i)
// {
// readLineF("%s%*%f%f%f", e, rx ,ry ,rz);
// newAtom(e, rx, ry, rz);
// }
// finaliseModel();
// rebond();
//
// # Create a grid associated to this model, and set it up with data we read previously
// newGrid(title);
// initGrid("regularxyz",nx,ny,nz);
// printf("Grid size (points) is : {%i,%i,%i}\n", nx, ny, nz);
// printf("Grid origin is : {%f,%f,%f}\n", origin.x, origin.y, origin.z);
// gridOrigin(origin.x, origin.y, origin.z);
// gridAxes(x.x, x.y, x.z, y.x, y.y, y.z, z.x, z.y, z.z);
//
// # Volumetric data (five points per line)
// for (i=1; i<=nx; ++i)
// {
// for (j=1; j<=ny; ++j)
// {
// for (k=1; k<=nz; ++k)
// {
// if (!nextArg(data)) error("Error reading point {%i,%i,%i} from file.\n", i,j,k);
// addGridPoint(i, j, k, data);
// }
// }
// }
// finaliseGrid();
//}
//
//filter(type="importgrid", name="Gaussian Cube", nickname="cube", extension="cube", glob="*.cube", zmap="numeric", id=1)
//{
// # Variable declaration
// string e,title;
// int natoms,nx,ny,nz,i,j,k;
// vector origin, x,y,z;
// double data;
//
// # Lines 1-2: Comments (use first as title)
// getLine(title);
// skipLine();
//
// # Line 3: Number of atoms and coordinate origin of surface
// readLine(natoms, origin.x, origin.y, origin.z);
//
// # Lines 4-6: Number of voxels and axis vector
// readLine(nx, x.x, x.y, x.z);
// readLine(ny, y.x, y.y, y.z);
// readLine(nz, z.x, z.y, z.z);
//
// # Lines 7-(7+natoms) Molecule Definition
// skipLine(natoms);
//
// # Create a grid associated to this model, and set it up with data we read previously
// newGrid(title);
// initGrid("regularxyz",nx,ny,nz);
// printf("Grid size (points) is : {%i,%i,%i}\n", nx, ny, nz);
// printf("Grid origin is : {%f,%f,%f}\n", origin.x, origin.y, origin.z);
// gridOrigin(origin.x, origin.y, origin.z);
// gridAxes(x.x, x.y, x.z, y.x, y.y, y.z, z.x, z.y, z.z);
//
// # Volumetric data (five points per line)
// for (i=1; i<=nx; ++i)
// {
// for (j=1; j<=ny; ++j)
// {
// for (k=1; k<=nz; ++k)
// {
// if (!nextArg(data)) error("Error reading point {%i,%i,%i} from file.\n", i,j,k);
// addGridPoint(i, j, k, data);
// }
// }
// }
// finaliseGrid();
//}
//
// Lines 1-2: Comments (use first as title)
QString name;
if (!fileParser_.readLine(name)) return false;
fileParser_.skipLines(1);

// Line 3: Number of atoms and coordinate origin of surface
if (!fileParser_.parseLine()) return false;
int nAtoms = fileParser_.argi(0);
Vec3<double> origin = fileParser_.arg3d(1);

// Lines 4-6: Number of voxels and axis vector
Vec3<int> nXYZ;
if (!fileParser_.parseLine()) return false;
nXYZ.x = fileParser_.argi(0);
double xFactor = nXYZ.x < 0 ? 1.0 : ANGBOHR;
Vec3<double> xAxis = fileParser_.arg3d(1);
nXYZ.y = fileParser_.argi(0);
double yFactor = nXYZ.y < 0 ? 1.0 : ANGBOHR;
Vec3<double> yAxis = fileParser_.arg3d(1);
nXYZ.z = fileParser_.argi(0);
double zFactor = nXYZ.z < 0 ? 1.0 : ANGBOHR;
Vec3<double> zAxis = fileParser_.arg3d(1);

// Lines 7-(7+natoms) Molecule Definition (SKIP)
fileParser_.skipLines(nAtoms);

// Create new grid in the target model
Grid* grid = createGrid(targetModel());
grid->setName(fileParser_.filename());

grid->initialise(Grid::RegularXYZData, nXYZ);
Messenger::print("Grid size (points) is : {%i,%i,%i}\n", nXYZ.x, nXYZ.y, nXYZ.z);
Messenger::print("Grid origin is : {%f,%f,%f}\n", origin.x, origin.y, origin.z);

grid->setOrigin(origin);
Matrix axes;
axes.setColumn(0, xAxis * xFactor, 0.0);
axes.setColumn(1, yAxis * yFactor, 0.0);
axes.setColumn(2, zAxis * zFactor, 0.0);
grid->setAxes(axes);

// Read in volumetric data
QString arg;
for (int i=0; i<nXYZ.x; ++i)
{
for (int j=0; j<nXYZ.y; ++j)
{
for (int k=0; k<nXYZ.z; ++k)
{
if (!fileParser_.readNextArg(arg))
{
Messenger::error("Failed to read grid point (%i,%i,%i) from cube file.\n", i+1, j+1, k+1);
return false;
}

grid->setNextData(arg.toDouble());
}
}
}

return true;
}

Expand Down
11 changes: 7 additions & 4 deletions src/plugins/io_cube/cubemodel_funcs.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ int CubeModelPlugin::category() const
// Name of plugin
QString CubeModelPlugin::name() const
{
return QString("Cube (dlputils) 3D probability density");
return QString("Gaussian cube file (including atomic coordinate data)");
}

// Nickname of plugin
Expand All @@ -79,7 +79,7 @@ bool CubeModelPlugin::enabled() const
// Description (long name) of plugin
QString CubeModelPlugin::description() const
{
return QString("Import/export for dlputils Cube files");
return QString("Import/export for Gaussian-format cube files");
}

// Related file extensions
Expand Down Expand Up @@ -123,9 +123,11 @@ bool CubeModelPlugin::importData()
nXYZ.x = fileParser_.argi(0);
double xFactor = nXYZ.x < 0 ? 1.0 : ANGBOHR;
Vec3<double> xAxis = fileParser_.arg3d(1);
if (!fileParser_.parseLine()) return false;
nXYZ.y = fileParser_.argi(0);
double yFactor = nXYZ.y < 0 ? 1.0 : ANGBOHR;
Vec3<double> yAxis = fileParser_.arg3d(1);
if (!fileParser_.parseLine()) return false;
nXYZ.z = fileParser_.argi(0);
double zFactor = nXYZ.z < 0 ? 1.0 : ANGBOHR;
Vec3<double> zAxis = fileParser_.arg3d(1);
Expand All @@ -140,7 +142,7 @@ bool CubeModelPlugin::importData()
{
if (!fileParser_.parseLine()) return false;

r = fileParser_.arg3d(1);
r = fileParser_.arg3d(2);
r.x *= xFactor;
r.y *= yFactor;
r.z *= zFactor;
Expand All @@ -165,6 +167,7 @@ bool CubeModelPlugin::importData()
axes.setColumn(1, yAxis * yFactor, 0.0);
axes.setColumn(2, zAxis * zFactor, 0.0);
grid->setAxes(axes);
axes.print();

// Read in volumetric data
QString arg;
Expand All @@ -174,7 +177,7 @@ bool CubeModelPlugin::importData()
{
for (int k=0; k<nXYZ.z; ++k)
{
if (!fileParser_.readArg(arg))
if (!fileParser_.readNextArg(arg))
{
Messenger::error("Failed to read grid point (%i,%i,%i) from cube file.\n", i+1, j+1, k+1);
return false;
Expand Down

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