Pull in PME net charge background correction

ipynb-kotlin/ffx.json

@@ -100,6 +100,7 @@
     "jakarta.activation-api-2.1.3.jar",
     "jakarta.xml.bind-api-4.0.2.jar",
     "javaparser-core-3.26.4.jar",
+    "javaparser-core-3.27.0.jar",
     "javax.annotation-api-1.3.2.jar",
     "jaxb-core-4.0.3.jar",
     "jaxb-runtime-4.0.3.jar",

modules/algorithms/src/main/groovy/ffx/algorithms/groovy/BAR.groovy

@@ -112,11 +112,11 @@ class BAR extends AlgorithmsScript {
   private boolean sortedArc = false
 
   @Option(names = ["--ss", "--startSnapshot"], paramLabel = "0",
-      description = "Start at this snapshot when reading in Tinker BAR files.")
+      description = "Start at this snapshot when reading in Tinker BAR files (indexed from 0).")
   private int startingSnapshot = 0
 
   @Option(names = ["--es", "--endSnapshot"], paramLabel = "0",
-      description = "End at this snapshot when reading in Tinker BAR files.")
+      description = "End at this snapshot when reading in Tinker BAR files (indexed from 0).")
   private int endingSnapshot = 0
 
   /**

modules/numerics/src/main/java/ffx/numerics/fft/Complex3DParallel.java

@@ -331,6 +331,7 @@ public Complex3DParallel(int nX, int nY, int nZ, ParallelTeam parallelTeam,
       useSIMD = false;
     }
 
+    // Do not pack FFTs by default for now.
     packFFTs = false;
     String pack = System.getProperty("fft.packFFTs", Boolean.toString(packFFTs));
     try {
@@ -360,11 +361,13 @@ public Complex3DParallel(int nX, int nY, int nZ, ParallelTeam parallelTeam,
       fftZ[i] = new Complex(nZ, dataLayout1D, internalImZ, nY);
       fftZ[i].setUseSIMD(useSIMD);
     }
-    if (!localZTranspose) {
-      work3D = new double[2 * nX * nY * nZ];
-    } else {
+
+    if (localZTranspose) {
       work3D = null;
+    } else {
+      work3D = new double[2 * nX * nY * nZ];
     }
+
     fftRegion = new FFTRegion();
     ifftRegion = new IFFTRegion();
     convRegion = new ConvolutionRegion();
@@ -488,6 +491,7 @@ public void initTiming() {
 
   /**
    * Get the timing string.
+   *
    * @return The timing string.
    */
   public String timingString() {
@@ -1030,11 +1034,15 @@ private class TransposeLoop extends IntegerForLoop {
     public void run(final int lb, final int ub) {
       for (int x = lb; x <= ub; x++) {
         for (int z = 0; z < nZ; z++) {
+          int inputOffset = x * nextX + z * nextZ;
+          int workOffset = x * trNextX + z * trNextZ;
           for (int y = 0; y < nY; y++) {
-            double real = input[x * nextX + y * nextY + z * nextZ];
-            double imag = input[x * nextX + y * nextY + z * nextZ + im];
-            work3D[y * trNextY + z * trNextZ + x * trNextX] = real;
-            work3D[y * trNextY + z * trNextZ + x * trNextX + internalImZ] = imag;
+            int inputIndex = inputOffset + y * nextY;
+            double real = input[inputIndex];
+            double imag = input[inputIndex + im];
+            int workIndex = workOffset + y * trNextY;
+            work3D[workIndex] = real;
+            work3D[workIndex + internalImZ] = imag;
           }
         }
       }
@@ -1082,11 +1090,15 @@ private class UnTransposeLoop extends IntegerForLoop {
     public void run(final int lb, final int ub) {
       for (int x = 0; x < nX; x++) {
         for (int y = 0; y < nY; y++) {
+          int workOffset = x * trNextX + y * trNextY;
+          int inputOffset = x * nextX + y * nextY;
           for (int z = lb; z <= ub; z++) {
-            double real = work3D[y * trNextY + z * trNextZ + x * trNextX];
-            double imag = work3D[y * trNextY + z * trNextZ + x * trNextX + internalImZ];
-            input[x * nextX + y * nextY + z * nextZ] = real;
-            input[x * nextX + y * nextY + z * nextZ + im] = imag;
+            int workIndex = workOffset + z * trNextZ;
+            double real = work3D[workIndex];
+            double imag = work3D[workIndex + internalImZ];
+            int inputIndex = inputOffset + z * nextZ;
+            input[inputIndex] = real;
+            input[inputIndex + im] = imag;
           }
         }
       }

modules/numerics/src/test/java/ffx/numerics/fft/Complex3DParallelTest.java

@@ -45,6 +45,7 @@
 import java.util.Random;
 
 import ffx.utilities.FFXTest;
+import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
@@ -101,6 +102,11 @@ public void setUp() {
     }
   }
 
+  @After
+  public void after() throws Exception {
+    parallelTeam.shutdown();
+  }
+
   /** Test of convolution method, of class Complex3D. */
   @Test
   public void testConvolution() {

modules/numerics/src/test/java/ffx/numerics/fft/Real3DParallelTest.java

@@ -45,6 +45,7 @@
 import java.util.Random;
 
 import ffx.utilities.FFXTest;
+import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
@@ -108,6 +109,11 @@ public void setUp() {
     }
   }
 
+  @After
+  public void after() throws Exception {
+    parallelTeam.shutdown();
+  }
+
   /** Test of convolution method, of class Real3DParallel. */
   @Test
   public void testConvolution() {

modules/pj/src/main/java/edu/rit/pj/KillRegion.java

@@ -55,9 +55,14 @@
  * @author Jacob Litman
  */
 public class KillRegion extends ParallelRegion {
+
     /** {@inheritDoc} */
     @Override
     public void run() throws Exception {
-        // Does precisely nothing save exist.
+        // Empty run method.
+        ParallelTeamThread currentThread = getCurrentThread();
+        Thread thread = currentThread.getThread();
+        long totalThreads = ParallelTeamThread.totalThreads.getAndDecrement();
+        // System.out.printf(" Killing team %s thread %s of %d\n", currentThread.myTeam, thread, totalThreads);
     }
 }

modules/pj/src/main/java/edu/rit/pj/PJProperties.java

@@ -233,6 +233,26 @@ public static int getPjNt() {
         return k;
     }
 
+    /**
+     * Determine whether a {@linkplain ParallelTeam} should use virtual threads.
+     * <p>
+     * If the <code>"pj.vt"</code> Java system property is true, then virtual threads
+     * will be used. If the property is false or not specified, then the
+     * program will use platform threads.
+     * <p>
+     * The default is false, meaning that the program will use platform threads.
+     * <p>
+     * @return true if the program should use virtual threads, false otherwise.
+     */
+    public static boolean getPjVt() {
+        String pjVtProperty = System.getProperty("pj.vt");
+        if (pjVtProperty != null) {
+            return Boolean.parseBoolean(pjVtProperty);
+        } else {
+            return false; // Default is false
+        }
+    }
+
     /**
      * Determine the schedule for a parallel loop in an SMP parallel program.
      * This is the schedule that will be used if the parallel for loop has a

modules/pj/src/main/java/edu/rit/pj/ParallelConstruct.java

@@ -148,16 +148,13 @@ ParallelTeamThread getCurrentThread() {
         if (myTeam == null) {
             throw new IllegalStateException("ParallelConstruct.getCurrentThread(): No parallel team executing");
         }
-        try {
-            ParallelTeamThread current = (ParallelTeamThread) Thread.currentThread();
-            if (current.myTeam != this.myTeam) {
-                throw new IllegalStateException("ParallelConstruct.getCurrentThread(): Current thread is not executing this parallel construct");
+        Thread currentThread = Thread.currentThread();
+        for (ParallelTeamThread teamThread : myTeam.myThread) {
+            if (teamThread.getThread() == currentThread) {
+                return teamThread;
             }
-            return current;
-        } catch (ClassCastException exc) {
-            throw new IllegalStateException("ParallelConstruct.getCurrentThread(): Current thread is not a parallel team thread",
-                    exc);
         }
+        throw new IllegalStateException("ParallelConstruct.getCurrentThread(): Current thread is not executing this parallel construct");
     }
 
-}
+}

modules/pj/src/main/java/edu/rit/pj/ParallelTeam.java

@@ -162,7 +162,7 @@ public final void execute(ParallelRegion theRegion)
 
         // Record parallel region.
         myRegion = theRegion;
-        myExceptionMap = new ConcurrentHashMap<Integer, Throwable>(K, 0.75f, K);
+        myExceptionMap = new ConcurrentHashMap<>(K, 0.75f, K);
         theRegion.myTeam = this;
 
         try {

modules/pj/src/main/java/edu/rit/pj/ParallelTeamThread.java

@@ -44,6 +44,7 @@
 //******************************************************************************
 package edu.rit.pj;
 
+import edu.rit.pj.reduction.SharedLong;
 import java.util.concurrent.Semaphore;
 
 /**
@@ -54,9 +55,9 @@
  * @version 20-Dec-2007
  */
 class ParallelTeamThread
-        extends Thread {
+        implements Runnable {
 
-// Hidden data members.
+    // Hidden data members.
     // Reference to the parallel team.
     ParallelTeam myTeam;
 
@@ -86,29 +87,64 @@ class ParallelTeamThread
     // Exception thrown while setting up a parallel construct, or null if none.
     volatile Throwable myConstructException;
 
+    // The thread instance
+    private final Thread thread;
+
+    /**
+     * Number of threads created by the ParallelTeamThread constructor.
+     */
+    public static SharedLong totalThreads = new SharedLong(0);
+
     // 128 bytes of extra padding to avert cache interference.
     private long p0, p1, p2, p3, p4, p5, p6, p7;
     private long p8, p9, pa, pb, pc, pd, pe, pf;
 
 // Exported constructors.
+
     /**
      * Construct a new parallel team thread.
      *
-     * @param theTeam Parallel team to which this thread belongs.
+     * @param theTeam  Parallel team to which this thread belongs.
      * @param theIndex Index of this thread within the team.
      */
     public ParallelTeamThread(ParallelTeam theTeam,
-            int theIndex) {
+                              int theIndex) {
         myTeam = theTeam;
         myIndex = theIndex;
-        setDaemon(true);
-        start();
+
+        String name = "ParallelTeamThread-" + theIndex;
+
+        boolean isVirtual = PJProperties.getPjVt();
+        if (isVirtual) {
+            // Create a virtual thread (all virtual threads are daemon threads).
+            thread = Thread.ofVirtual().name(name).unstarted(this);
+        } else {
+            // Create a new thread for this parallel team thread.
+            thread = Thread.ofPlatform().name(name).unstarted(this);
+            thread.setDaemon(true);
+        }
+
+        long numThreads = totalThreads.incrementAndGet();
+        // System.out.printf(" Creating team %s thread %s out of %d.\n", myTeam, name, numThreads);
+
+        thread.start();
     }
 
 // Exported operations.
+
+    /**
+     * Get the underlying thread.
+     *
+     * @return The Thread instance
+     */
+    public Thread getThread() {
+        return thread;
+    }
+
     /**
      * Run this parallel team thread.
      */
+    @Override
     public void run() {
         for (;;) {
             // Wait until released by the main thread.
@@ -120,6 +156,8 @@ public void run() {
                 } catch (Exception ex) {
                     System.err.printf("Error exiting parallel team thread: %s%n", ex);
                 }
+
+                // Exit the for loop and run method, which will allow threads to be garbage collected.
                 break;
             }
 

modules/potential/src/main/groovy/ffx/potential/groovy/PrepareSpaceGroups.groovy

@@ -222,8 +222,8 @@ class PrepareSpaceGroups extends PotentialScript {
         continue
       }
 
-      logger.info(format("\n Preparing %s (CSD percent: %7.4f, PDB Rank: %d)",
-          spacegroup2.shortName, getCCDCPercent(num), getPDBRank(spacegroup)))
+      logger.info(format("\n Preparing %d %s (CSD percent: %7.4f, PDB Rank: %d)",
+          num, spacegroup2.shortName, getCCDCPercent(num), getPDBRank(spacegroup)))
 
       // Create the directory.
       String sgDirName = spacegroup2.shortName.replace('/', '_')

modules/potential/src/main/java/ffx/potential/extended/ExtendedSystem.java

@@ -149,6 +149,7 @@ public class ExtendedSystem implements Potential {
      */
     private final double LYStitrBiasMag;
     private final List<Constraint> constraints;
+    public final boolean useTotalChargeCorrection;
     private final boolean doBias;
     private final boolean doElectrostatics;
     private final boolean doPolarization;
@@ -317,6 +318,7 @@ public ExtendedSystem(MolecularAssembly mola, double pH, final File esvFile) {
         doElectrostatics = properties.getBoolean("esv.elec", true);
         doBias = properties.getBoolean("esv.bias", true);
         doPolarization = properties.getBoolean("esv.polarization", true);
+        useTotalChargeCorrection = properties.getBoolean("esv.total.charge.correction", false);
         thetaFriction = properties.getDouble("esv.friction", ExtendedSystem.THETA_FRICTION);
         thetaMass = properties.getDouble("esv.mass", ExtendedSystem.THETA_MASS);