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 static java.util.Arrays.fill;
41
42 import edu.rit.pj.ParallelTeam;
43 import ffx.crystal.Crystal;
44 import ffx.potential.bonded.Atom;
45 import ffx.potential.nonbonded.SpatialDensityLoop;
46 import ffx.potential.nonbonded.SpatialDensityRegion;
47
48 /**
49 * This class implements a spatial decomposition based on partitioning a grid into octants. The
50 * over-ridden "selectAtoms" method selects atoms that are not in the asymmetric unit, but are
51 * within the supplied cutoff radius.
52 *
53 * @author Michael J. Schnieders
54 * @since 1.0
55 */
56 public class BulkSolventDensityRegion extends SpatialDensityRegion {
57
58 private final BulkSolventList bulkSolventList;
59
60 /**
61 * Constructor for BulkSolventDensityRegion.
62 *
63 * @param gX a int.
64 * @param gY a int.
65 * @param gZ a int.
66 * @param grid an array of double.
67 * @param basisSize a int.
68 * @param nSymm a int.
69 * @param minWork a int.
70 * @param threadCount a int.
71 * @param crystal a {@link ffx.crystal.Crystal} object.
72 * @param atoms an array of {@link ffx.potential.bonded.Atom} objects.
73 * @param coordinates an array of double.
74 * @param cutoff a double.
75 * @param parallelTeam a {@link edu.rit.pj.ParallelTeam} object.
76 */
77 public BulkSolventDensityRegion(
78 int gX,
79 int gY,
80 int gZ,
81 double[] grid,
82 int basisSize,
83 int nSymm,
84 int minWork,
85 int threadCount,
86 Crystal crystal,
87 Atom[] atoms,
88 double[][][] coordinates,
89 double cutoff,
90 ParallelTeam parallelTeam) {
91 super(gX, gY, gZ, grid, basisSize, nSymm, minWork, threadCount, crystal, atoms, coordinates);
92
93 // Asymmetric unit atoms never selected by this class.
94 fill(select[0], false);
95 bulkSolventList = new BulkSolventList(crystal, atoms, cutoff, parallelTeam);
96 }
97
98 /** {@inheritDoc} */
99 @Override
100 public void run() {
101 int ti = getThreadIndex();
102 int actualWork1 = actualWork - 1;
103 SpatialDensityLoop loop = spatialDensityLoop[ti];
104 try {
105 execute(0, actualWork1, loop.setOctant(0));
106 // Fractional chunks along the C-axis.
107 if (nC > 1) {
108 execute(0, actualWork1, loop.setOctant(1));
109 // Fractional chunks along the B-axis.
110 if (nB > 1) {
111 execute(0, actualWork1, loop.setOctant(2));
112 execute(0, actualWork1, loop.setOctant(3));
113 // Fractional chunks along the A-axis.
114 if (nA > 1) {
115 execute(0, actualWork1, loop.setOctant(4));
116 execute(0, actualWork1, loop.setOctant(5));
117 execute(0, actualWork1, loop.setOctant(6));
118 execute(0, actualWork1, loop.setOctant(7));
119 }
120 }
121 }
122 } catch (Exception e) {
123 logger.severe(e.toString());
124 }
125 }
126
127 /** {@inheritDoc} */
128 @Override
129 public void selectAtoms() {
130 bulkSolventList.buildList(coordinates, select, false);
131 }
132 }