1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2024.
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.potential.nonbonded;
39
40 import edu.rit.pj.IntegerForLoop;
41 import java.util.ArrayList;
42
43 /**
44 * The SliceLoop class is used to parallelize placing onto a 3D grid
45 *
46 * <p>1) Multipoles using B-splines or
47 *
48 * <p>2) Diffraction form factors.
49 *
50 * <p>Each "slice" of the grid (i.e. a fixed value of the z-coordinate) is operated on by only a
51 * single thread to logically enforce atomic updates of grid magnitudes.
52 *
53 * @author Armin Avdic
54 */
55 public abstract class SliceLoop extends IntegerForLoop {
56
57 protected boolean rebuildList = false;
58 protected ArrayList<Integer> buildListA = new ArrayList<>();
59 protected ArrayList<Integer> buildListS = new ArrayList<>();
60 protected SliceRegion sliceRegion;
61 private int nAtoms;
62 private int nSymm;
63
64 /**
65 * Constructor for SliceLoop.
66 *
67 * @param nAtoms a int.
68 * @param nSymm a int.
69 * @param sliceRegion a {@link ffx.potential.nonbonded.SliceRegion} object.
70 */
71 public SliceLoop(int nAtoms, int nSymm, SliceRegion sliceRegion) {
72 this.nAtoms = nAtoms;
73 this.nSymm = nSymm;
74 this.sliceRegion = sliceRegion;
75 }
76
77 /**
78 * checkList.
79 *
80 * @param zAtListBuild an array of {@link int} objects.
81 * @param buff a int.
82 * @return a boolean.
83 */
84 public boolean checkList(int[][] zAtListBuild, int buff) {
85 return false;
86 }
87
88 /**
89 * Apply electron density "as normal" for an atom, but check that the z index is within the
90 * supplied bounds (inclusive).
91 *
92 * @param iSymm the SymOp to apply.
93 * @param iAtom the index of the Atom to put onto the grid.
94 * @param lb the lower bound along the z-axis.
95 * @param ub the upper bound along the z-axis.
96 */
97 public abstract void gridDensity(int iSymm, int iAtom, int lb, int ub);
98
99 /** {@inheritDoc} */
100 @Override
101 public void run(int lb, int ub) throws Exception {
102 for (int iSymm = 0; iSymm < nSymm; iSymm++) {
103 for (int iAtom = 0; iAtom < nAtoms; iAtom++) {
104 if (sliceRegion.select[iSymm][iAtom]) {
105 gridDensity(iSymm, iAtom, lb, ub);
106 }
107 }
108 }
109 }
110
111 /**
112 * saveZValues.
113 *
114 * @param zAtListBuild an array of {@link int} objects.
115 */
116 public void saveZValues(int[][] zAtListBuild) {}
117
118 /**
119 * setNsymm
120 *
121 * @param nSymm a int.
122 */
123 public void setNsymm(int nSymm) {
124 this.nSymm = nSymm;
125 assert (nSymm <= sliceRegion.nSymm);
126 }
127
128 /**
129 * Setter for the field <code>rebuildList</code>.
130 *
131 * @param rebuildList a boolean.
132 */
133 void setRebuildList(boolean rebuildList) {
134 this.rebuildList = rebuildList;
135 }
136 }