This file is indexed.

/usr/include/trilinos/Galeri_GalerkinVariational.h is in libtrilinos-galeri-dev 12.4.2-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
// @HEADER
// ************************************************************************
//
//           Galeri: Finite Element and Matrix Generation Package
//                 Copyright (2006) ETHZ/Sandia Corporation
//
// Under terms of Contract DE-AC04-94AL85000, there is a non-exclusive
// license for use of this work by or on behalf of the U.S. Government.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 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.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "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 SANDIA CORPORATION OR THE
// 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.
//
// Questions about Galeri? Contact Marzio Sala (marzio.sala _AT_ gmail.com)
//
// ************************************************************************
// @HEADER

#ifndef GALERI_GALERKINVARIATIONAL_H
#define GALERI_GALERKINVARIATIONAL_H

/*!
 * \file Galeri_GalerkinVariational.h
 */

#include "Galeri_Workspace.h"
#include "Galeri_AbstractVariational.h"

namespace Galeri {
namespace FiniteElements {

/*!
 * \class GalerkinVariational
 *
 * \brief Defines a pure Galerkin variational form of a scalar PDE.
 *
 * This class defines a pure Galerkin variational form of a second order,
 * symmetric scalar PDE, discretized using Lagrange finite elements. The class is
 * templated with an AbstractQuadrature class, which will be used to 
 * specify the quadrature formula, and the values of test and basis functions
 * at the quadrature node. The constructor requires function pointers, that
 * specify the values of the coefficients.
 *
 * \author Marzio Sala, SNL 9214.
 *
 * \date Last updated on Apr-05.
 */

template<class T>
class GalerkinVariational : public AbstractVariational, public T
{
public:

  //! Constructor.
  GalerkinVariational(const int NumQuadratureNodes,
                      double (*diff)(const double&, const double&, const double&),
                      double (*source)(const double&, const double&, const double&),
                      double (*force)(const double&, const double&, const double&),
                      double (*bc)(const double&, const double&, const double&, const int&),
                      int (*bc_type)(const int&)):
    T(NumQuadratureNodes),
    diff_(diff),
    source_(source),
    force_(force),
    bc_(bc),
    bc_type_(bc_type)
  {}

  //! Destructor.  
  ~GalerkinVariational() {}

  //! Evaluates the diffusion coefficient at point (x, y, z).
  inline double diff(const double x, const double y, const double z) const
  {
    return (diff_(x, y, z));
  }

  //! Evaluates the source term at point (x, y, z).
  inline double source(const double x, const double y, const double z) const
  {
    return (source_(x, y, z));
  }

  //! Evaluates the force term at point (x, y, z).
  inline double force(const double x, const double y, const double z) const
  {
    return (force_(x, y, z));
  }

  //! Integrates the variational form and the right-hand side.
  virtual int IntegrateOverElement(const AbstractVariational& Variational,
				   const double* x, const double* y, const double* z,
                                   const double* data,
				   double* ElementMatrix, double* ElementRHS) const
  {
    double xq, yq, zq;
    int size = T::NumPhiFunctions();
    //double h = data[0];
    
    // zero out local matrix and rhs
    
    for (int i = 0 ; i < size * size ; i++) ElementMatrix[i] = 0.0;
    for (int i = 0 ; i < size ; i++)        ElementRHS[i] = 0.0;

    // cycle over all quadrature nodes

    for (int ii = 0 ; ii < T::NumQuadrNodes() ; ii++) 
    {
      T::ComputeQuadrNodes(ii,x, y, z, xq, yq, zq);
      T::ComputeJacobian(ii,x, y, z);
      T::ComputeDerivatives(ii);

      for (int i = 0 ; i < T::NumPhiFunctions() ; ++i) 
      {
        for (int j = 0 ; j < T::NumPsiFunctions() ; ++j) 
        {
          ElementMatrix[j + size * i] +=
            T::QuadrWeight(ii) * T::DetJacobian(ii) * 
            Variational.LHS(T::Phi(i), T::Psi(j), T::PhiX(i), T::PsiX(j),
                            T::PhiY(i), T::PsiY(j), T::PhiZ(i), T::PsiZ(j),
                            xq, yq, zq);
        }
        ElementRHS[i] += T::QuadrWeight(ii) * T::DetJacobian(ii) *
          Variational.RHS(T::Psi(i), T::PsiX(i), T::PsiY(i), T::PsiZ(i), 
                          xq, yq, zq);
      }
    }

    return 0;
  }

  //! Computes the norm of the numerical solution over an element.
  virtual int ElementNorm(const double* LocalSol, const double* x, 
                          const double* y, const double* z, double* Norm) const
  {
    double xq, yq, zq;
    //double exact[4];

    for (int ii = 0 ; ii < T::NumQuadrNodes() ; ii++) 
    {
      T::ComputeQuadrNodes(ii,x, y, z, xq, yq, zq );
      T::ComputeJacobian(ii,x, y, z);
      T::ComputeDerivatives(ii);

      double GlobalWeight = T::QuadrWeight(ii) * T::DetJacobian(ii);

      double sol      = 0.0, sol_derx = 0.0;
      double sol_dery = 0.0, sol_derz = 0.0;

      for (int k = 0 ; k < T::NumPhiFunctions() ; ++k)
      {
        sol      += T::Phi(k)  * LocalSol[k];
        sol_derx += T::PhiX(k) * LocalSol[k];
        sol_dery += T::PhiY(k) * LocalSol[k];
        sol_derz += T::PhiZ(k) * LocalSol[k];
      }

      Norm[0] += GlobalWeight*sol*sol;
      Norm[1] += GlobalWeight*(sol_derx*sol_derx +
                               sol_dery*sol_dery +
                               sol_derz*sol_derz);
    }

    return 0;
  }

  //! Computes the norm of the exact solution over an element.
  virtual int ElementNorm(int (*ExactSolution)(double, double, double, double *),
			  const double* x, const double* y, const double* z,
			  double* Norm) const
  {
    double xq, yq, zq;
    double exact[4];

    for (int ii = 0 ; ii < T::NumQuadrNodes() ; ii++) 
    {
      T::ComputeQuadrNodes(ii, x, y, z, xq, yq, zq );
      T::ComputeJacobian(ii, x, y, z);
      T::ComputeDerivatives(ii);

      double GlobalWeight = T::QuadrWeight(ii) * T::DetJacobian(ii);

      (*ExactSolution)(xq, yq, zq, exact);

      Norm[0] += GlobalWeight * exact[0] * exact[0];
      Norm[1] += GlobalWeight * (exact[1] * exact[1] +
                                 exact[2] * exact[2] +
                                 exact[3] * exact[3]);
    }

    return 0;
  }
  
  //! Computes the norm of the error over an element.
  virtual int ElementNorm(const double* LocalSol,
			  int (*ExactSolution)(double, double, double, double *),
			  const double* x, const double* y, const double* z, double * Norm) const
  {
    double xq, yq, zq;
    double exact[4];

    for (int ii = 0 ; ii < T::NumQuadrNodes() ; ii++) 
    {
      T::ComputeQuadrNodes(ii, x, y, z, xq, yq, zq );
      T::ComputeJacobian(ii, x, y, z);
      T::ComputeDerivatives(ii);

      double GlobalWeight = T::QuadrWeight(ii) * T::DetJacobian(ii);

      double diff      = 0.0, diff_derx = 0.0;
      double diff_dery = 0.0, diff_derz = 0.0;

      for (int k = 0 ; k < T::NumPhiFunctions() ; ++k) 
      {
        diff      += T::Phi(k)  * LocalSol[k];
        diff_derx += T::PhiX(k) * LocalSol[k];
        diff_dery += T::PhiY(k) * LocalSol[k];
        diff_derz += T::PhiZ(k) * LocalSol[k];
      }

      (*ExactSolution)(xq, yq, zq,exact);

      diff      -= exact[0];
      diff_derx -= exact[1];
      diff_dery -= exact[2];
      diff_derz -= exact[3];

      Norm[0] += GlobalWeight * diff * diff;
      Norm[1] += GlobalWeight * (diff_derx * diff_derx +
                                 diff_dery * diff_dery +
                                 diff_derz * diff_derz);
    } 
    return(0);
  }

  //! Evaluates the left-hand side at point (x, y, z).
  inline double LHS(const double Phi, const double Psi,
                    const double PhiX, const double PsiX,
                    const double PhiY, const double PsiY,
                    const double PhiZ, const double PsiZ,
                    const double x, const double y, const double z) const
  {
    return(diff(x,y,z) * PhiX * PsiX +
           diff(x,y,z) * PhiY * PsiY +
           diff(x,y,z) * PhiZ * PsiZ +
           source(x,y,z) * Phi * Psi);
  }

  //! Evaluates the right-hand side at point (x, y, z).
  inline double RHS(const double Psi, const double PsiX, 
                    const double PsiY, const double PsiZ,
                    const double x, const double y, const double z) const
  {
    return(force(x,y,z)*Psi);
  }

  //! Returns the boundary condition type of the specified patch.
  int BC(const int PatchID) const
  {
    return(bc_type_(PatchID));
  }

  //! Returns the value of the boundary condition at point (x, y, z).
  double BC(const double x, const double y, const double z, const int PatchID) const
  {
    return(bc_(x, y, z, PatchID));
  }

private:
  double (*diff_)(const double& x, const double& y, const double& z);
  double (*source_)(const double& x, const double& y, const double& z);
  double (*force_)(const double& x, const double& y, const double& z);
  double (*bc_)(const double& x, const double& y, const double& z, const int& Patch);
  int (*bc_type_)(const int& Patch);
};

} // namespace FiniteElements
} // namespace Galeri
#endif