Examples with CompositeConfiguration org.apache.commons.configuration.CompositeConfiguration used on opensource projects

Example 11 with CompositeConfiguration

use of org.apache.commons.configuration.CompositeConfiguration in project ffx by mjschnie.

the class CrystalReciprocalSpaceTest method test1N7SPermanent.

/**
 * Test of permanent method, of class CrystalReciprocalSpace.
 */
@Test
public void test1N7SPermanent() {
    String filename = "ffx/xray/structures/1N7S.pdb";
    int index = filename.lastIndexOf(".");
    String name = filename.substring(0, index);
    // load the structure
    ClassLoader cl = this.getClass().getClassLoader();
    File structure = new File(cl.getResource(filename).getPath());
    PotentialsUtils potutil = new PotentialsUtils();
    MolecularAssembly mola = potutil.open(structure);
    CompositeConfiguration properties = mola.getProperties();
    Crystal crystal = new Crystal(39.767, 51.750, 132.938, 90.00, 90.00, 90.00, "P212121");
    Resolution resolution = new Resolution(1.45);
    ReflectionList reflectionList = new ReflectionList(crystal, resolution);
    DiffractionRefinementData refinementData = new DiffractionRefinementData(properties, reflectionList);
    mola.finalize(true, mola.getForceField());
    ForceFieldEnergy energy = mola.getPotentialEnergy();
    List<Atom> atomList = mola.getAtomList();
    Atom[] atomArray = atomList.toArray(new Atom[atomList.size()]);
    // set up FFT and run it
    ParallelTeam parallelTeam = new ParallelTeam();
    CrystalReciprocalSpace crs = new CrystalReciprocalSpace(reflectionList, atomArray, parallelTeam, parallelTeam);
    crs.computeAtomicDensity(refinementData.fc);
    // tests
    ComplexNumber b = new ComplexNumber(-828.584, -922.704);
    HKL hkl = reflectionList.getHKL(1, 1, 4);
    ComplexNumber a = refinementData.getFc(hkl.index());
    System.out.println("1 1 4: " + a.toString() + " | " + b.toString() + " | " + a.divides(b).toString());
    assertEquals("1 1 4 reflection should be correct", -753.4722104328416, a.re(), 0.0001);
    assertEquals("1 1 4 reflection should be correct", -1012.1341308707799, a.im(), 0.0001);
    b.re(-70.4582);
    b.im(-486.142);
    hkl = reflectionList.getHKL(2, 1, 10);
    a = refinementData.getFc(hkl.index());
    System.out.println("2 1 10: " + a.toString() + " | " + b.toString() + " | " + a.divides(b).toString());
    assertEquals("2 1 10 reflection should be correct", -69.39660884054359, a.re(), 0.0001);
    assertEquals("2 1 10 reflection should be correct", -412.0147625765328, a.im(), 0.0001);
}

Example 12 with CompositeConfiguration

use of org.apache.commons.configuration.CompositeConfiguration in project ffx by mjschnie.

the class CIFFilterTest method testCIFFilter3DYC.

@Test
public void testCIFFilter3DYC() {
    String filename = "ffx/xray/structures/3DYC.ent";
    ClassLoader cl = this.getClass().getClassLoader();
    File cifFile = new File(cl.getResource(filename).getPath());
    // load any properties associated with it
    CompositeConfiguration properties = Keyword.loadProperties(cifFile);
    CIFFilter cifFilter = new CIFFilter();
    ReflectionList reflectionList = cifFilter.getReflectionList(cifFile);
    assertNotNull(" Reflection list should not be null", reflectionList);
    DiffractionRefinementData refinementData = new DiffractionRefinementData(properties, reflectionList);
    assertTrue(" CIF data not read in correctly", cifFilter.readFile(cifFile, reflectionList, refinementData, properties));
    HKL hkl = reflectionList.getHKL(58, 0, 13);
    assertEquals("58 0 13 F", 99.7, refinementData.getF(hkl.index()), 0.01);
    assertEquals("58 0 13 sigF", 69.7, refinementData.getSigF(hkl.index()), 0.01);
    assertEquals("58 0 13 freeR value", 1, refinementData.freer[hkl.index()]);
    hkl = reflectionList.getHKL(28, 20, 5);
    assertEquals("28 20 5 F", 428.1, refinementData.getF(hkl.index()), 0.01);
    assertEquals("28 20 5 sigF", 10.1, refinementData.getSigF(hkl.index()), 0.01);
    assertEquals("28 20 5 freeR value", 0, refinementData.freer[hkl.index()]);
}

Example 13 with CompositeConfiguration

use of org.apache.commons.configuration.CompositeConfiguration in project ffx by mjschnie.

the class MolecularDynamics method assemblyInfo.

protected void assemblyInfo() {
    assemblies.stream().parallel().forEach((ainfo) -> {
        MolecularAssembly mola = ainfo.getAssembly();
        CompositeConfiguration aprops = ainfo.props;
        File file = mola.getFile();
        String filename = FilenameUtils.removeExtension(file.getAbsolutePath());
        File archFile = ainfo.archiveFile;
        if (archFile == null) {
            archFile = new File(filename + ".arc");
            ainfo.archiveFile = XYZFilter.version(archFile);
        }
        if (ainfo.pdbFile == null) {
            String extName = FilenameUtils.getExtension(file.getName());
            if (extName.toLowerCase().startsWith("pdb")) {
                ainfo.pdbFile = file;
            } else {
                ainfo.pdbFile = new File(filename + ".pdb");
            }
        }
        if (ainfo.xyzFilter == null) {
            ainfo.xyzFilter = new XYZFilter(file, mola, mola.getForceField(), aprops);
        }
        if (ainfo.pdbFilter == null) {
            ainfo.pdbFilter = new PDBFilter(ainfo.pdbFile, mola, mola.getForceField(), aprops);
        }
    });
}

Example 14 with CompositeConfiguration

use of org.apache.commons.configuration.CompositeConfiguration in project ffx by mjschnie.

the class AlgorithmUtils method md.

/**
 * Performs molecular dynamics on a MolecularAssembly.
 *
 * @param assembly the MolecularAssembly to do MD on.
 * @param nStep the number of MD steps.
 * @param timeStep the MD time step.
 * @param printInterval the time between logging statements.
 * @param saveInterval the time between saving restart files.
 * @param temperature the target temperature.
 * @param initVelocities if true, reset velocities from a Maxwell
 * distribution.
 * @param dyn a dynamics restart.
 */
@Override
public void md(MolecularAssembly assembly, int nStep, double timeStep, double printInterval, double saveInterval, double temperature, boolean initVelocities, File dyn) {
    if (assembly == null) {
        logger.info(" No active system to minimize.");
    } else {
        CompositeConfiguration properties = Keyword.loadProperties(assembly.getFile());
        MolecularDynamics molecularDynamics = new MolecularDynamics(assembly, assembly.getPotentialEnergy(), properties, null, ThermostatEnum.BUSSI, IntegratorEnum.BEEMAN);
        molecularDynamics.dynamic(nStep, timeStep, printInterval, saveInterval, temperature, initVelocities, dyn);
    }
}

Example 15 with CompositeConfiguration

use of org.apache.commons.configuration.CompositeConfiguration in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method loadPlatform.

/**
 * Load an OpenMM Platform
 */
private void loadPlatform(Platform requestedPlatform) {
    // Print out the OpenMM Version.
    Pointer version = OpenMM_Platform_getOpenMMVersion();
    logger.log(Level.INFO, " OpenMM Version: {0}", version.getString(0));
    // Print out the OpenMM plugin directory.
    Pointer pluginDir = OpenMM_Platform_getDefaultPluginsDirectory();
    String pluginDirString = pluginDir.getString(0);
    if (SystemUtils.IS_OS_WINDOWS) {
        pluginDirString = pluginDirString + "/plugins";
    }
    logger.log(Level.INFO, " OpenMM Plugin Dir: {0}", pluginDirString);
    /**
     * Load plugins and print out plugins.
     *
     * Call the method twice to avoid a bug where not all platforms are list
     * after the first call.
     */
    PointerByReference plugins = OpenMM_Platform_loadPluginsFromDirectory(pluginDirString);
    OpenMM_StringArray_destroy(plugins);
    plugins = OpenMM_Platform_loadPluginsFromDirectory(pluginDirString);
    int numPlugins = OpenMM_StringArray_getSize(plugins);
    logger.log(Level.INFO, " Number of OpenMM Plugins: {0}", numPlugins);
    boolean cuda = false;
    for (int i = 0; i < numPlugins; i++) {
        String pluginString = stringFromArray(plugins, i);
        logger.log(Level.INFO, "  Plugin: {0}", pluginString);
        if (pluginString.toUpperCase().contains("AMOEBACUDA")) {
            cuda = true;
        }
    }
    OpenMM_StringArray_destroy(plugins);
    /**
     * Extra logging to print out plugins that failed to load.
     */
    if (logger.isLoggable(Level.FINE)) {
        PointerByReference pluginFailers = OpenMM_Platform_getPluginLoadFailures();
        int numFailures = OpenMM_StringArray_getSize(pluginFailers);
        for (int i = 0; i < numFailures; i++) {
            String pluginString = stringFromArray(pluginFailers, i);
            logger.log(Level.FINE, " Plugin load failure: {0}", pluginString);
        }
        OpenMM_StringArray_destroy(pluginFailers);
    }
    int numPlatforms = OpenMM_Platform_getNumPlatforms();
    logger.log(Level.INFO, " Number of OpenMM Platforms: {0}", numPlatforms);
    /**
     * for (int i = 0; i < numPlatforms; i++) { PointerByReference
     * currentPlatform = OpenMM_Platform_getPlatform(i); Pointer
     * platformName = OpenMM_Platform_getName(currentPlatform);
     * logger.log(Level.INFO, " Platform: {0}", platformName.getString(0));
     * OpenMM_Platform_destroy(currentPlatform); }
     */
    String defaultPrecision = "mixed";
    String precision = molecularAssembly.getForceField().getString(ForceField.ForceFieldString.PRECISION, defaultPrecision).toLowerCase();
    precision = precision.replace("-precision", "");
    switch(precision) {
        case "double":
        case "mixed":
        case "single":
            logger.info(String.format(" Using precision level %s", precision));
            break;
        default:
            logger.info(String.format(" Could not interpret precision level %s, defaulting to %s", precision, defaultPrecision));
            precision = defaultPrecision;
            break;
    }
    Comm world = Comm.world();
    int size = world.size();
    int defDeviceIndex = 0;
    if (size > 1) {
        int rank = world.rank();
        CompositeConfiguration props = molecularAssembly.getProperties();
        // 0/no-arg would indicate "just put everything on device specified by CUDA_DEVICE".
        // TODO: Get the number of CUDA devices from the CUDA API as the alternate default.
        int numCudaDevices = props.getInt("numCudaDevices", 0);
        if (numCudaDevices > 0) {
            defDeviceIndex = rank % numCudaDevices;
            logger.info(String.format(" Placing energy from rank %d on device %d", rank, defDeviceIndex));
        }
    }
    int deviceID = molecularAssembly.getForceField().getInteger(ForceField.ForceFieldInteger.CUDA_DEVICE, defDeviceIndex);
    String deviceIDString = Integer.toString(deviceID);
    if (cuda && requestedPlatform != Platform.OMM_REF) {
        platform = OpenMM_Platform_getPlatformByName("CUDA");
        OpenMM_Platform_setPropertyDefaultValue(platform, pointerForString("CudaDeviceIndex"), pointerForString(deviceIDString));
        OpenMM_Platform_setPropertyDefaultValue(platform, pointerForString("Precision"), pointerForString(precision));
        logger.info(String.format(" Selected OpenMM AMOEBA CUDA Platform (Device ID: %d)", deviceID));
    } else {
        platform = OpenMM_Platform_getPlatformByName("Reference");
        logger.info(" Selected OpenMM AMOEBA Reference Platform");
    }
}