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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 2001-2024.
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 RowLoop 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 "row" of the grid (i.e. fixed values of the z and y-coordinates) 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 RowLoop extends IntegerForLoop {
56  
57    protected ArrayList<Integer> buildListA = new ArrayList<>();
58    protected ArrayList<Integer> buildListS = new ArrayList<>();
59    protected RowRegion rowRegion;
60    protected boolean rebuildList = false;
61    private int nAtoms;
62    private int nSymm;
63  
64    /**
65     * Constructor for RowLoop.
66     *
67     * @param nAtoms a int.
68     * @param nSymm a int.
69     * @param rowRegion a {@link ffx.potential.nonbonded.RowRegion} object.
70     */
71    public RowLoop(int nAtoms, int nSymm, RowRegion rowRegion) {
72      this.nAtoms = nAtoms;
73      this.nSymm = nSymm;
74      this.rowRegion = rowRegion;
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 y and z indeces are within
90     * the 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 for the y and z-axes.
95     * @param ub the upper bound for the y and z-axes.
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 (rowRegion.select[iSymm][iAtom]) {
105           gridDensity(iSymm, iAtom, lb, ub);
106         }
107       }
108     }
109   }
110 
111   /**
112    * saveZYValues.
113    *
114    * @param zAtListBuild an array of {@link int} objects.
115    */
116   public void saveZYValues(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 <= rowRegion.nSymm);
126   }
127 }