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1   // ******************************************************************************
2   //
3   // Title:       Force Field X.
4   // Description: Force Field X - Software for Molecular Biophysics.
5   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
6   //
7   // This file is part of Force Field X.
8   //
9   // Force Field X is free software; you can redistribute it and/or modify it
10  // under the terms of the GNU General Public License version 3 as published by
11  // the Free Software Foundation.
12  //
13  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
14  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
15  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
16  // details.
17  //
18  // You should have received a copy of the GNU General Public License along with
19  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
20  // Place, Suite 330, Boston, MA 02111-1307 USA
21  //
22  // Linking this library statically or dynamically with other modules is making a
23  // combined work based on this library. Thus, the terms and conditions of the
24  // GNU General Public License cover the whole combination.
25  //
26  // As a special exception, the copyright holders of this library give you
27  // permission to link this library with independent modules to produce an
28  // executable, regardless of the license terms of these independent modules, and
29  // to copy and distribute the resulting executable under terms of your choice,
30  // provided that you also meet, for each linked independent module, the terms
31  // and conditions of the license of that module. An independent module is a
32  // module which is not derived from or based on this library. If you modify this
33  // library, you may extend this exception to your version of the library, but
34  // you are not obligated to do so. If you do not wish to do so, delete this
35  // exception statement from your version.
36  //
37  // ******************************************************************************
38  package ffx.xray;
39  
40  import edu.rit.pj.ParallelTeam;
41  import ffx.crystal.Crystal;
42  import ffx.potential.bonded.Atom;
43  import ffx.potential.nonbonded.SliceRegion;
44  
45  import java.util.logging.Level;
46  import java.util.logging.Logger;
47  
48  import static java.util.Arrays.fill;
49  
50  /**
51   * This class implements a spatial decomposition based on partitioning a grid into octants. The
52   * over-ridden "selectAtoms" method selects atoms that are not in the asymmetric unit, but are
53   * within the supplied cutoff radius.
54   *
55   * @author Michael J. Schnieders
56   * @since 1.0
57   */
58  public class BulkSolventSliceRegion extends SliceRegion {
59  
60    /** Constant <code>logger</code> */
61    protected static final Logger logger = Logger.getLogger(BulkSolventSliceRegion.class.getName());
62  
63    private final BulkSolventList bulkSolventList;
64    private final int gZ;
65  
66    /**
67     * Constructor for BulkSolventDensityRegion.
68     *
69     * @param gX a int.
70     * @param gY a int.
71     * @param gZ a int.
72     * @param grid an array of double.
73     * @param nSymm a int.
74     * @param threadCount a int.
75     * @param crystal a {@link ffx.crystal.Crystal} object.
76     * @param atoms an array of {@link ffx.potential.bonded.Atom} objects.
77     * @param coordinates an array of double.
78     * @param cutoff a double.
79     * @param parallelTeam a {@link edu.rit.pj.ParallelTeam} object.
80     */
81    public BulkSolventSliceRegion(
82        int gX,
83        int gY,
84        int gZ,
85        double[] grid,
86        int nSymm,
87        int threadCount,
88        Crystal crystal,
89        Atom[] atoms,
90        double[][][] coordinates,
91        double cutoff,
92        ParallelTeam parallelTeam) {
93      super(gX, gY, gZ, grid, nSymm, threadCount, atoms, coordinates);
94      this.gZ = gZ;
95      // Asymmetric unit atoms never selected by this class.
96      fill(select[0], false);
97      bulkSolventList = new BulkSolventList(crystal, atoms, cutoff, parallelTeam);
98    }
99  
100   /** {@inheritDoc} */
101   @Override
102   public void run() {
103     try {
104       execute(0, gZ - 1, sliceLoop[getThreadIndex()]);
105     } catch (Exception e) {
106       String message = " Exception in BulkSolventSliceRegion.";
107       logger.log(Level.SEVERE, message, e);
108     }
109   }
110 
111   /** {@inheritDoc} */
112   @Override
113   public void selectAtoms() {
114     bulkSolventList.buildList(coordinates, select, false);
115   }
116 }