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 }