pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
  <artifactId>forcefieldx</artifactId>
  <build>
    <defaultGoal>install</defaultGoal>
    <pluginManagement>
      <!-- Explicitly define plugins for FFX module pom.xml files. -->
      <plugins>
        <!-- Group: io.github.git-commit-id -->
        <plugin>
          <groupId>io.github.git-commit-id</groupId>
          <artifactId>git-commit-id-maven-plugin</artifactId>
          <version>${git-commit-id.version}</version>
        </plugin>

        <!-- Group: org.apache.maven.plugins (default) -->
        <plugin>
          <artifactId>maven-antrun-plugin</artifactId>
          <version>${antrun.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-assembly-plugin</artifactId>
          <version>${assembly.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-changes-plugin</artifactId>
          <version>${changes.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-checkstyle-plugin</artifactId>
          <version>${checkstyle.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-clean-plugin</artifactId>
          <configuration>
            <filesets>
              <fileset>
                <directory>${basedir}/src/site/resources/scripts</directory>
              </fileset>
            </filesets>
          </configuration>
          <version>${clean.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-compiler-plugin</artifactId>
          <configuration>
            <compilerArgs>
              <arg>-Xlint:all,-serial,-processing,-this-escape</arg>
              <arg>-proc:none</arg>
              <arg>--add-modules</arg>
              <arg>jdk.incubator.vector</arg>
            </compilerArgs>
            <debug>true</debug>
            <source>${compileVersion}</source>
            <release>${compileVersion}</release>
            <useIncrementalCompilation>true</useIncrementalCompilation>
          </configuration>
          <version>${compiler.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-dependency-plugin</artifactId>
          <version>${dependency.version}</version>
          <inherited>true</inherited>
          <executions>
            <execution>
              <id>ffx-lib</id>
              <phase>package</phase>
              <goals>
                <goal>copy-dependencies</goal>
              </goals>
              <configuration>
                <outputDirectory>${basedir}/../../lib</outputDirectory>
                <overWriteReleases>false</overWriteReleases>
                <overWriteSnapshots>false</overWriteSnapshots>
                <overWriteIfNewer>true</overWriteIfNewer>
                <silent>true</silent>
              </configuration>
            </execution>
          </executions>
        </plugin>
        <plugin>
          <artifactId>maven-deploy-plugin</artifactId>
          <configuration>
            <deployAtEnd>true</deployAtEnd>
          </configuration>
          <version>${deploy.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-enforcer-plugin</artifactId>
          <version>${enforcer.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-install-plugin</artifactId>
          <configuration>
            <installAtEnd>true</installAtEnd>
          </configuration>
          <version>${install.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-jar-plugin</artifactId>
          <version>${jar.version}</version>
          <configuration>
            <skipIfEmpty>false</skipIfEmpty>
          </configuration>
        </plugin>
        <plugin>
          <artifactId>maven-jarsigner-plugin</artifactId>
          <version>${jarsigner.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-javadoc-plugin</artifactId>
          <configuration>
            <author>true</author>
            <failOnError>false</failOnError>
            <additionalOptions>
              <additionalOption>--add-modules jdk.incubator.vector</additionalOption>
            </additionalOptions>
            <doclint>all,-missing</doclint>
          </configuration>
          <version>${javadoc.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-jxr-plugin</artifactId>
          <version>${jxr.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-linkcheck-plugin</artifactId>
          <version>${linkcheck.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-pmd-plugin</artifactId>
          <version>${pmd.version}</version>
          <inherited>false</inherited>
        </plugin>
        <plugin>
          <artifactId>maven-project-info-reports-plugin</artifactId>
          <version>${project-info-reports.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-release-plugin</artifactId>
          <version>${release.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-resources-plugin</artifactId>
          <version>${resources.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-scm-plugin</artifactId>
          <version>${scm.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-site-plugin</artifactId>
          <version>${site.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-source-plugin</artifactId>
          <version>${source.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-surefire-plugin</artifactId>
          <configuration>
            <!-- forkCount>1</forkCount -->
            <trimStackTrace>false</trimStackTrace>
            <argLine>--add-modules jdk.incubator.vector</argLine>
          </configuration>
          <dependencies>
            <dependency>
              <artifactId>surefire-junit47</artifactId>
              <groupId>org.apache.maven.surefire</groupId>
              <version>${surefire.version}</version>
            </dependency>
          </dependencies>
          <version>${surefire.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-surefire-report-plugin</artifactId>
          <configuration>
            <aggregate>true</aggregate>
            <alwaysGenerateSurefireReport>true</alwaysGenerateSurefireReport>
            <linkXRef>true</linkXRef>
          </configuration>
          <dependencies>
            <dependency>
              <artifactId>surefire-junit47</artifactId>
              <groupId>org.apache.maven.surefire</groupId>
              <version>${surefire.version}</version>
            </dependency>
          </dependencies>
          <version>${surefire.version}</version>
        </plugin>
        <plugin>
          <artifactId>maven-wrapper-plugin</artifactId>
          <version>${wrapper.version}</version>
        </plugin>

        <!-- Group: org.asciidoctor -->
        <plugin>
          <groupId>org.asciidoctor</groupId>
          <artifactId>asciidoctor-maven-plugin</artifactId>
          <version>${asciidoc.version}</version>
        </plugin>

        <!-- Group: org.codehaus.gmavenplus -->
        <plugin>
          <groupId>org.codehaus.gmavenplus</groupId>
          <artifactId>gmavenplus-plugin</artifactId>
          <version>${gmavenplus.version}</version>
        </plugin>

        <!-- Group: org.codehaus.mojo -->
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>appassembler-maven-plugin</artifactId>
          <version>${appassembler.version}</version>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>exec-maven-plugin</artifactId>
          <version>${exec.version}</version>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>jdepend-maven-plugin</artifactId>
          <version>${jdepend.version}</version>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>properties-maven-plugin</artifactId>
          <version>${properties.version}</version>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>versions-maven-plugin</artifactId>
          <version>${versions.version}</version>
        </plugin>

        <!-- Group: org.jacoco -->
        <plugin>
          <groupId>org.jacoco</groupId>
          <artifactId>jacoco-maven-plugin</artifactId>
          <version>${jacoco.version}</version>
        </plugin>
      </plugins>
    </pluginManagement>
    <plugins>
      <plugin>
        <artifactId>maven-dependency-plugin</artifactId>
        <inherited>false</inherited>
        <executions>
          <execution>
            <id>ffx-lib</id>
            <!-- Prevent this plugin from running in the parent pom.xml. -->
            <phase>none</phase>
            <goals>
              <goal>copy-dependencies</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-enforcer-plugin</artifactId>
        <executions>
          <execution>
            <configuration>
              <rules>
                <banDuplicatePomDependencyVersions/>
                <!-- dependencyConvergence/ -->
                <!-- reactorModuleConvergence/ -->
                <requireJavaVersion>
                  <version>[25,26.1]</version>
                </requireJavaVersion>
                <requireMavenVersion>
                  <version>3.8</version>
                </requireMavenVersion>
                <requirePluginVersions/>
              </rules>
            </configuration>
            <goals>
              <goal>enforce</goal>
            </goals>
            <id>enforce-versions</id>
            <phase>initialize</phase>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-site-plugin</artifactId>
        <configuration>
          <generateSitemap>true</generateSitemap>
          <moduleExcludes>
            <moduleExclude>modules/codecov</moduleExclude>
          </moduleExcludes>
        </configuration>
        <inherited>true</inherited>
        <dependencies>
          <dependency>
            <groupId>org.asciidoctor</groupId>
            <artifactId>asciidoctor-parser-doxia-module</artifactId>
            <version>${asciidoc.version}</version>
          </dependency>
        </dependencies>
      </plugin>
      <plugin>
        <artifactId>maven-clean-plugin</artifactId>
        <configuration>
          <filesets>
            <fileset>
              <directory>lib</directory>
            </fileset>
            <fileset>
              <directory>groovy</directory>
            </fileset>
            <fileset>
              <directory>src/site/asciidoc/properties</directory>
            </fileset>
            <fileset>
              <directory>src/site/asciidoc/commands</directory>
            </fileset>
          </filesets>
        </configuration>
        <inherited>false</inherited>
      </plugin>
      <plugin>
        <artifactId>maven-assembly-plugin</artifactId>
        <configuration>
          <descriptors>
            <descriptor>src/assemble/bin.xml</descriptor>
          </descriptors>
          <finalName>ffx-${project.version}</finalName>
          <outputDirectory>${project.build.directory}/site</outputDirectory>
          <tarLongFileMode>posix</tarLongFileMode>
        </configuration>
        <executions>
          <execution>
            <goals>
              <goal>single</goal>
            </goals>
            <phase>site</phase>
          </execution>
        </executions>
        <inherited>false</inherited>
      </plugin>
      <plugin>
        <artifactId>exec-maven-plugin</artifactId>
        <configuration>
          <arguments>
            <argument>-ms1G</argument>
            <argument>-mx1G</argument>
            <argument>-classpath</argument>
            <argument>lib/*</argument>
            <!-- argument>-Djava.awt.headless=true</argument>
            <argument>-Dj3d.rend=noop</argument>
            <argument>ffx.Main</argument>
            <argument>Timer</argument>
            <argument>-n</argument>
            <argument>1000</argument>
            <argument>examples/ubiquitin.xyz</argument -->
            <argument>ffx.numerics.estimator.MultistateBennettAcceptanceRatio</argument>
          </arguments>
          <executable>java</executable>
        </configuration>
        <executions>
          <execution>
            <goals>
              <goal>exec</goal>
            </goals>
            <id>Run Force Field X</id>
          </execution>
        </executions>
        <groupId>org.codehaus.mojo</groupId>
        <inherited>false</inherited>
      </plugin>
      <plugin>
        <artifactId>maven-surefire-plugin</artifactId>
        <configuration>
          <!-- Less than 1G may lead to JVM out of memory exceptions. -->
          <!-- Jacoco agent details are within the property "jacoco.agent.ut.arg" -->
          <argLine>@{jacoco.agent.ut.arg} -Xms1G -Xmx1G -Djava.awt.headless=true -Dj3d.rend=noop --add-modules
            jdk.incubator.vector
          </argLine>
          <!-- useSystemClassLoader>false</useSystemClassLoader -->
          <excludes>
            <exclude>**/ParentEnergyTest</exclude>
          </excludes>
        </configuration>
        <dependencies>
          <dependency>
            <artifactId>surefire-junit47</artifactId>
            <groupId>org.apache.maven.surefire</groupId>
            <version>${surefire.version}</version>
          </dependency>
        </dependencies>
      </plugin>
      <!-- plugin>
          <artifactId>maven-pdf-plugin</artifactId>
          <version>1.2</version>
          <executions>
              <execution>
                  <id>pdf</id>
                  <phase>site</phase>
                  <goals>
                      <goal>pdf</goal>
                  </goals>
                  <configuration>
                      <outputDirectory>${project.reporting.outputDirectory}/site</outputDirectory>
                      <implementation>itext</implementation>
                  </configuration>
              </execution>
          </executions>
      </plugin -->
      <plugin>
        <groupId>io.github.git-commit-id</groupId>
        <artifactId>git-commit-id-maven-plugin</artifactId>
        <inherited>false</inherited>
        <executions>
          <execution>
            <id>get-the-git-infos</id>
            <goals>
              <goal>revision</goal>
            </goals>
            <phase>initialize</phase>
          </execution>
        </executions>
        <configuration>
          <verbose>false</verbose>
          <skipPoms>false</skipPoms>
          <injectAllReactorProjects>false</injectAllReactorProjects>
          <generateGitPropertiesFile>false</generateGitPropertiesFile>
          <generateGitPropertiesFilename>${basedir}/bin/git.properties</generateGitPropertiesFilename>
          <includeOnlyProperties>
            <includeOnlyProperty>git.commit.id.full</includeOnlyProperty>
            <includeOnlyProperty>git.total.commit.count</includeOnlyProperty>
          </includeOnlyProperties>
          <commitIdGenerationMode>full</commitIdGenerationMode>
        </configuration>
      </plugin>
      <plugin>
        <artifactId>properties-maven-plugin</artifactId>
        <executions>
          <execution>
            <configuration>
              <outputFile>${basedir}/bin/build.properties</outputFile>
            </configuration>
            <goals>
              <goal>write-project-properties</goal>
            </goals>
            <phase>initialize</phase>
          </execution>
        </executions>
        <groupId>org.codehaus.mojo</groupId>
        <inherited>false</inherited>
      </plugin>
      <plugin>
        <groupId>org.jacoco</groupId>
        <artifactId>jacoco-maven-plugin</artifactId>
        <configuration>
          <destFile>target/jacoco.exec</destFile>
          <!-- append>true</append -->
        </configuration>
        <executions>
          <execution>
            <goals>
              <goal>prepare-agent</goal>
            </goals>
            <configuration>
              <propertyName>jacoco.agent.ut.arg</propertyName>
              <skip>${jacoco.skip}</skip>
            </configuration>
          </execution>
          <!-- attached to Maven test phase -->
          <execution>
            <id>report</id>
            <phase>test</phase>
            <goals>
              <goal>report</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-antrun-plugin</artifactId>
        <inherited>false</inherited>
        <executions>
          <execution>
            <id>Create Keyword AsciiDoc Files</id>
            <phase>pre-site</phase>
            <goals>
              <goal>run</goal>
            </goals>
            <configuration>
              <target>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/ElectrostaticsFunctionalForm.adoc">
                  <header>== Electrostatics Functional Form</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/ElectrostaticsFunctionalForm">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/EnergyUnitConversion.adoc">
                  <header>== Energy Unit Conversion</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/EnergyUnitConversion">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/ImplicitSolvent.adoc">
                  <header>== Implicit Solvent</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/ImplicitSolvent">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/LocalGeometryFunctionalForm.adoc">
                  <header>== Local Geometry Functional Form</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/LocalGeometryFunctionalForm">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/NonBondedCutoff.adoc">
                  <header>== Non-Bonded Cutoff</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/NonBondedCutoff">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/ParticleMeshEwald.adoc">
                  <header>== Particle-Mesh Ewald</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/ParticleMeshEwald">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/PotentialFunctionParameter.adoc">
                  <header>== Potential Function Parameter</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/PotentialFunctionParameter">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/PotentialFunctionSelection.adoc">
                  <header>== Potential Function Selection</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/PotentialFunctionSelection">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/UnitCellAndSpaceGroup.adoc">
                  <header>== Unit Cell and Space Group</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/UnitCellAndSpaceGroup">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/VanDerWaalsFunctionalForm.adoc">
                  <header>== Van Der Waals Functional Form</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/VanDerWaalsFunctionalForm">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
                <concat destfile="${project.basedir}/src/site/asciidoc/properties/StructuralRefinement.adoc">
                  <header>== Structural Refinement</header>
                  <fileset erroronmissingdir="false"
                           dir="${project.basedir}/src/site/asciidoc/properties/StructuralRefinement">
                    <include name="*.adoc"/>
                  </fileset>
                </concat>
              </target>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>
  <ciManagement>
    <notifiers>
      <notifier>
        <configuration>
          <address>michael-schnieders@uiowa.edu</address>
        </configuration>
        <sendOnError>true</sendOnError>
        <sendOnFailure>true</sendOnFailure>
        <sendOnSuccess>false</sendOnSuccess>
        <sendOnWarning>false</sendOnWarning>
        <type>mail</type>
      </notifier>
    </notifiers>
    <system>Github Actions</system>
    <url>https://github.com/SchniedersLab/forcefieldx/actions</url>
  </ciManagement>
  <contributors>
    <contributor>
      <email>hernan-bernabe@uiowa.edu</email>
      <name>Hernan Bernabe</name>
      <roles>
        <role>
          Contributions to Monte Carlo Orthogonal Space Sampling.
        </role>
      </roles>
      <timezone>-5</timezone>
    </contributor>
    <contributor>
      <email>jhauer@health.ucsd.edu</email>
      <name>Jill J. Hauer</name>
      <organization>Post-Doctoral Fellow, UCSD</organization>
      <organizationUrl>https://ucsd.edu</organizationUrl>
      <roles>
        <role>
          Pathogenicity Prediction and Thermodynamics of Missense Mutations for Rare Renal Diseases
        </role>
      </roles>
      <timezone>-5</timezone>
    </contributor>
    <contributor>
      <email>tollefson.will@gmail.com</email>
      <name>William T. A. Tollefson</name>
      <organization>Software Engineer, Collins Aerospace</organization>
      <organizationUrl>https://www.collinsaerospace.com</organizationUrl>
      <roles>
        <role>
          Contributions to many-body side-chain repacking and modeling of missense mutations.
        </role>
      </roles>
      <timezone>-5</timezone>
    </contributor>
    <contributor>
      <email>ava-lynn@uiowa.edu</email>
      <name>Ava M. Lynn</name>
      <organization>Physician, Uniformed Services University of the Health Sciences</organization>
      <organizationUrl>https://www.usuhs.edu</organizationUrl>
      <roles>
        <role>
          Contributions to implementation of rotamer libraries.
        </role>
      </roles>
      <timezone>-4</timezone>
    </contributor>
    <contributor>
      <email>ian.nessler@abbvie.com</email>
      <name>Ian J. Nessler</name>
      <organization>Senior Scientist, AbbVie</organization>
      <organizationUrl>https://www.abbvie.com</organizationUrl>
      <roles>
        <role>
          Drug Crystal Structure, Thermodynamics and Solubility
        </role>
      </roles>
      <timezone>-7</timezone>
    </contributor>
    <contributor>
      <email>julia-park@gmail.com</email>
      <name>Jooyeon "Julia" Park</name>
      <organization>Dentist, The U. of Pennsylvania</organization>
      <organizationUrl>https://www.upenn.edu</organizationUrl>
      <roles>
        <role>
          Drug Crystal Structure, Thermodynamics and Solubility
        </role>
      </roles>
      <timezone>-4</timezone>
    </contributor>
    <contributor>
      <email>pren@mail.utexas.edu</email>
      <name>Pengyu Ren</name>
      <organization>Associate Professor, The U. of Texas at Austin</organization>
      <organizationUrl>https://www.utexas.edu</organizationUrl>
      <roles>
        <role>AMOEBA Force Field</role>
      </roles>
      <timezone>-5</timezone>
    </contributor>
    <contributor>
      <email>oversnow@gmail.com</email>
      <name>Zhen Xia</name>
      <organization>Postdoc, Ren Lab, The U. of Texas at Austin</organization>
      <organizationUrl>https://biomol.bme.utexas.edu/lab/</organizationUrl>
      <roles>
        <role>AMOEBA force field</role>
      </roles>
      <timezone>-5</timezone>
    </contributor>
    <contributor>
      <email>jwu@mail.utexas.edu</email>
      <name>Johnny Wu</name>
      <organization>Scientist at Genentech</organization>
      <organizationUrl>https://www.gene.com</organizationUrl>
      <roles>
        <role>Automatic AMOEBA Parameterization</role>
      </roles>
      <timezone>-7</timezone>
    </contributor>
    <contributor>
      <email>chuanjiewu@gmail.com</email>
      <name>Chuanjie Wu</name>
      <organization>Scientist at Schrodinger</organization>
      <roles>
        <role>AMOEBA force field</role>
      </roles>
      <timezone>-4</timezone>
    </contributor>
  </contributors>
  <dependencies>
    <dependency>
      <artifactId>groovy-all</artifactId>
      <groupId>org.apache.groovy</groupId>
      <type>pom</type>
      <version>${groovy-all.version}</version>
    </dependency>
    <dependency>
      <groupId>com.github.spotbugs</groupId>
      <artifactId>spotbugs-annotations</artifactId>
      <version>${spotbugs.version}</version>
      <optional>true</optional>
    </dependency>
    <dependency>
      <groupId>org.graalvm.polyglot</groupId>
      <artifactId>polyglot</artifactId>
      <version>${graal.version}</version>
    </dependency>
    <dependency>
      <groupId>org.graalvm.polyglot</groupId>
      <artifactId>python</artifactId>
      <version>${graal.version}</version>
      <scope>runtime</scope>
      <type>pom</type>
    </dependency>
    <dependency>
      <groupId>org.graalvm.python</groupId>
      <artifactId>python-embedding</artifactId>
      <version>${graal.version}</version>
    </dependency>
  </dependencies>
  <description>Polyglot Software for Molecular Biophysics</description>
  <developers>
    <developer>
      <email>michael-schnieders@uiowa.edu</email>
      <id>michael.schnieders</id>
      <name>Michael J. Schnieders</name>
      <organization>Associate Professor, The U. of Iowa</organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>Director of Force Field X</role>
      </roles>
      <timezone>-5</timezone>
    </developer>
    <developer>
      <email>tim.fenn@gmail.com</email>
      <id>fenn</id>
      <name>Timothy D. Fenn</name>
      <organization>Associate Director at Prevail Therapeutics</organization>
      <organizationUrl>https://www.prevailtherapeutics.com</organizationUrl>
      <roles>
        <role>Chief Crystallograper</role>
      </roles>
      <timezone>-7</timezone>
    </developer>
    <developer>
      <email>mallory-tollefson@uiowa.edu</email>
      <id>mrtollefson</id>
      <name>Mallory R. Tollefson</name>
      <organization>Instructor, Biochemistry and Molecular Biology, The U. of Iowa</organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>
          Pathogenicity Prediction of Missense Mutations Implicated in Hearing Loss
        </role>
        <role>
          Global Optimization Side-Chain Conformations using a Many-Body Expansion
        </role>
      </roles>
      <timezone>-5</timezone>
    </developer>
    <developer>
      <email>aaron-nessler@uiowa.edu</email>
      <id>anessler</id>
      <name>Aaron Nessler</name>
      <organization>Biomedical Engineering Graduate Student, Schnieders Lab, The U. of Iowa
      </organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>
          Thermodynamics of Crystals
        </role>
      </roles>
      <timezone>-5</timezone>
    </developer>
    <developer>
      <email>andrew-thiel@uiowa.edu</email>
      <id>andthiel</id>
      <name>Andrew Thiel</name>
      <organization>Biomedical Engineering Graduate Student, Schnieders Labs, The U. of Iowa
      </organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>
          Constant pH Simulation methods.
        </role>
      </roles>
      <timezone>-5</timezone>
    </developer>
    <developer>
      <email>rae-corrigan@uiowa.edu</email>
      <id>rcorrigan</id>
      <name>Rae Corrigan</name>
      <organization>Postdoctoral Fellow, Schnieders Lab, The U. of Iowa</organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>
          Generalized Kirkwood Continuum Solvation for the AMOEBA Force Field
        </role>
      </roles>
      <timezone>-5</timezone>
    </developer>
    <developer>
      <email>rose-gogal@uiowa.edu</email>
      <id>rgogal</id>
      <name>Rose Gogal</name>
      <organization>Biomedical Engineering PhD student, Schnieders Lab, The U. of Iowa</organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>
          Pathogenicity Prediction of Missense Mutations Implicated in Hearing Loss
        </role>
        <role>
          Global Optimization Side-Chain Protonation States using a Many-Body Expansion
        </role>
      </roles>
      <timezone>-5</timezone>
    </developer>
    <developer>
      <email>jacob-m-miller@uiowa.edu</email>
      <id>jmiller99</id>
      <name>Jacob Miller</name>
      <organization>Biomedical Engineering Graduate Student, Schnieders Lab, The U. of Iowa</organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>
          Pathogenicity Prediction of Missense Mutations Implicated in Autism Spectrum Disorder
        </role>
        <role>
          Generalized Kirkwood Continuum Solvation for the Nucleic Acids
        </role>
      </roles>
      <timezone>-5</timezone>
    </developer>
    <developer>
      <email>matthew-speranza@uiowa.edu</email>
      <id>msperanza</id>
      <name>Matthew Speranza</name>
      <organization>Biomedical Engineering Student, Schnieders Labs, The U. of Iowa
      </organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>
          Constant pH Simulation methods.
        </role>
        <role>
          Crystal Structure Prediction.
        </role>
      </roles>
      <timezone>-5</timezone>
    </developer>
    <developer>
      <email>leah-cousineau@uiowa.edu</email>
      <id>lmcousineau</id>
      <name>Leah Cousineau</name>
      <organization>Biochemistry and Molecular Biology Student, Schnieders Labs, The U. of Iowa
      </organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>
          Pathogenicity Prediction of Missense Mutations Implicated in Deafness.
        </role>
      </roles>
      <timezone>-5</timezone>
    </developer>
    <developer>
      <email>jacob.m.litman@gmail.com</email>
      <id>jmlitman</id>
      <name>Jacob M. Litman</name>
      <organization>Post-Doctoral Fellow, Ren Lab, The U. of Texas at Austin
      </organization>
      <organizationUrl>https://www.uiowa.edu</organizationUrl>
      <roles>
        <role>
          Global Optimization using Many-Body Expansions
        </role>
        <role>
          Indirect Free Energy Methods
        </role>
      </roles>
      <timezone>-5</timezone>
    </developer>
  </developers>
  <distributionManagement>
    <downloadUrl>https://ffx.biochem.uiowa.edu/download.html</downloadUrl>
    <repository>
      <id>bintray-mjschnie-maven</id>
      <name>mjschnie-maven</name>
      <url>${release.repo}</url>
    </repository>
    <site>
      <id>Website</id>
      <name>Force Field X Website Deploy Location</name>
      <url>${website.repo}</url>
    </site>
    <snapshotRepository>
      <id>Snapshots</id>
      <name>Local Maven SNAPSHOT Repository</name>
      <uniqueVersion>false</uniqueVersion>
      <url>${snapshot.repo}</url>
    </snapshotRepository>
  </distributionManagement>
  <groupId>edu.uiowa.eng.ffx</groupId>
  <inceptionYear>2001</inceptionYear>
  <issueManagement>
    <system>GitHub Issues</system>
    <url>https://github.com/SchniedersLab/forcefieldx/issues</url>
  </issueManagement>
  <licenses>
    <license>
      <distribution>manual</distribution>
      <name>GPL version 3 with Classpath Exception</name>
      <url>https://www.gnu.org/licenses/gpl-3.0-standalone.html</url>
      <comments>
        Force Field X is free software; you can redistribute it and/or modify it
        under the terms of the GNU General Public License version 3 as published by
        the Free Software Foundation.

        Force Field X is distributed in the hope that it will be useful, but WITHOUT
        ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
        FOR A PARTICULAR PURPOSE. See the GNU General Public License below for more details.

        Linking Force Field X statically or dynamically with other modules is making a
        combined work based on this library. Thus, the terms and conditions of the
        GNU General Public License cover the whole combination.

        As a special exception, the copyright holders of this library give you
        permission to link this library with independent modules to produce an
        executable, regardless of the license terms of these independent modules, and
        to copy and distribute the resulting executable under terms of your choice,
        provided that you also meet, for each linked independent module, the terms
        and conditions of the license of that module. An independent module is a
        module which is not derived from or based on this library. If you modify this
        library, you may extend this exception to your version of the library, but
        you are not obligated to do so. If you do not wish to do so, delete this
        exception statement from your version.
      </comments>
    </license>
  </licenses>
  <modelVersion>4.0.0</modelVersion>
  <modules>
    <module>modules/algorithms</module>
    <module>modules/codecov</module>
    <module>modules/crystal</module>
    <module>modules/openmm</module>
    <module>modules/numerics</module>
    <module>modules/pj</module>
    <module>modules/potential</module>
    <module>modules/refinement</module>
    <module>modules/ui</module>
    <module>modules/utilities</module>
  </modules>
  <name>Force Field X</name>
  <organization>
    <!-- This is used to generate the Copyright on the website.
    Module authors can use their name. -->
    <name>Michael J. Schnieders</name>
    <url>https://ffx.biochem.uiowa.edu</url>
  </organization>
  <packaging>pom</packaging>
  <pluginRepositories>
    <pluginRepository>
      <id>central</id>
      <name>Central Repository</name>
      <url>https://repo.maven.apache.org/maven2</url>
      <layout>default</layout>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
      <releases>
        <updatePolicy>daily</updatePolicy>
      </releases>
    </pluginRepository>
  </pluginRepositories>
  <profiles>
    <profile>
      <id>python</id>
      <activation>
        <activeByDefault>false</activeByDefault>
      </activation>
      <build>
        <plugins>
          <plugin>
            <groupId>org.graalvm.python</groupId>
            <artifactId>graalpy-maven-plugin</artifactId>
            <version>${graal.version}</version>
            <inherited>false</inherited>
            <executions>
              <execution>
                <configuration>
                  <packages>
                    <package>numpy==2.2.4</package>
                    <package>torch==2.7.0</package>
                  </packages>
                  <externalDirectory>
                    ${project.basedir}/python-resources
                  </externalDirectory>
                </configuration>
                <goals>
                  <goal>process-graalpy-resources</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>
  <properties>
    <asciidoc.version>3.2.0</asciidoc.version>
    <antlr4.version>4.13.2</antlr4.version>
    <antrun.version>3.2.0</antrun.version>
    <appassembler.version>2.1.0</appassembler.version>
    <assembly.skipAssembly>false</assembly.skipAssembly>
    <assembly.version>3.8.0</assembly.version>
    <biojava.version>7.2.4</biojava.version>
    <cdk.version>2.11</cdk.version>
    <changes.jira.skip>true</changes.jira.skip>
    <changes.version>2.12.1</changes.version>
    <checkstyle.skip>true</checkstyle.skip>
    <checkstyle.version>3.6.0</checkstyle.version>
    <ciftools-java.version>8.0.1</ciftools-java.version>
    <clean.version>3.5.0</clean.version>
    <clover.version>4.4.1</clover.version>
    <commons-beanutils.version>1.11.0</commons-beanutils.version>
    <commons-collections4.version>4.4</commons-collections4.version>
    <commons-configuration2.version>2.13.0</commons-configuration2.version>
    <commons-io.version>2.21.0</commons-io.version>
    <commons-lang3.version>3.20.0</commons-lang3.version>
    <commons-math3.version>3.6.1</commons-math3.version>
    <commons-text.version>1.15.0</commons-text.version>
    <!-- Control the source version -->
    <compileVersion>25</compileVersion>
    <compiler.version>3.15.0</compiler.version>
    <dependency.version>3.10.0</dependency.version>
    <dependencyDetails>false</dependencyDetails>
    <deploy.version>3.1.4</deploy.version>
    <enforcer.version>3.6.2</enforcer.version>
    <exec.version>3.6.3</exec.version>
    <failIfNoTests>false</failIfNoTests>
    <fastutil.version>8.5.12</fastutil.version>
    <!-- Version of FFX  -->
    <ffx.version>1.0.0</ffx.version>
    <git-commit-id.version>9.0.2</git-commit-id.version>
    <gmavenplus.version>4.3.1</gmavenplus.version>
    <graal.version>25.0.2</graal.version>
    <groovy-all.version>5.0.4</groovy-all.version>
    <guava.version>33.5.0-jre</guava.version>
    <install.version>3.1.4</install.version>
    <jacoco.version>0.8.14</jacoco.version>
    <jacoco.skip>true</jacoco.skip>
    <jar.version>3.5.0</jar.version>
    <jarsigner.version>3.1.0</jarsigner.version>
    <javaparser.version>3.28.0</javaparser.version>
    <java3d.version>1.7.2</java3d.version>
    <javadoc.version>3.12.0</javadoc.version>
    <jakarta-xml.version>4.0.5</jakarta-xml.version>
    <jdepend.version>2.2.0</jdepend.version>
    <jna.version>5.18.1</jna.version>
    <jogamp-fat.version>2.6.0</jogamp-fat.version>
    <jopenmm.version>8.3.4</jopenmm.version>
    <junit.version>4.13.2</junit.version>
    <jxr.version>3.6.0</jxr.version>
    <linkcheck.skip>true</linkcheck.skip>
    <linkcheck.version>1.2</linkcheck.version>
    <log4j.version>2.25.3</log4j.version>
    <maven.build.timestamp.format>MM-dd-yyyy</maven.build.timestamp.format>
    <maven.javadoc.skip>false</maven.javadoc.skip>
    <maven.jxr.skip>false</maven.jxr.skip>
    <MRJToolkitStubs.version>1.0</MRJToolkitStubs.version>
    <picocli.version>4.7.7</picocli.version>
    <pmd.version>3.28.0</pmd.version>
    <project-info-reports.version>3.9.0</project-info-reports.version>
    <!-- Setting the source encoding is required for builds that are platform independent. -->
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <properties.version>1.3.0</properties.version>
    <!-- Default locations for deploying a release (can be over-ridden by settings.xml) -->
    <release.repo>file:release</release.repo>
    <release.version>3.3.1</release.version>
    <resources.version>3.4.0</resources.version>
    <scm.version>2.2.1</scm.version>
    <site.version>3.21.0</site.version>
    <skipSurefireReport>false</skipSurefireReport>
    <skipTests>true</skipTests>
    <!-- Default locations for deploying snapshots (can be over-ridden by settings.xml) -->
    <snapshot.repo>file:lib</snapshot.repo>
    <source.version>3.4.0</source.version>
    <spotbugs.version>4.9.8</spotbugs.version>
    <surefire.version>3.5.5</surefire.version>
    <!-- Control the target JRE version -->
    <targetVersion>25</targetVersion>
    <timestamp>${maven.build.timestamp}</timestamp>
    <tornado.version>1.1.0</tornado.version>
    <!-- This is the javax.vecmath version used by CDK -->
    <vecmath.version>1.5.2</vecmath.version>
    <versions.version>2.21.0</versions.version>
    <!-- Default locations for deploying the website (can be over-ridden by settings.xml) -->
    <website.repo>file:website</website.repo>
    <wrapper.version>3.3.4</wrapper.version>
  </properties>
  <reporting>
    <plugins>
      <plugin>
        <artifactId>versions-maven-plugin</artifactId>
        <groupId>org.codehaus.mojo</groupId>
        <reportSets>
          <reportSet>
            <reports>
              <report>plugin-updates-aggregate-report</report>
              <report>dependency-updates-aggregate-report</report>
            </reports>
          </reportSet>
        </reportSets>
        <version>${versions.version}</version>
      </plugin>
      <plugin>
        <artifactId>maven-project-info-reports-plugin</artifactId>
        <configuration>
          <dependencyDetailsEnabled>${dependencyDetails}</dependencyDetailsEnabled>
          <showAvatarImages>true</showAvatarImages>
        </configuration>
        <reportSets>
          <reportSet>
            <reports>
              <report>ci-management</report>
              <report>dependencies</report>
              <report>dependency-convergence</report>
              <report>dependency-management</report>
              <report>distribution-management</report>
              <report>issue-management</report>
              <report>licenses</report>
              <report>mailing-lists</report>
              <report>modules</report>
              <report>plugin-management</report>
              <report>plugins</report>
              <report>team</report>
              <report>scm</report>
              <report>summary</report>
            </reports>
          </reportSet>
        </reportSets>
        <version>${project-info-reports.version}</version>
      </plugin>
      <plugin>
        <artifactId>maven-javadoc-plugin</artifactId>
        <configuration>
          <failOnError>false</failOnError>
          <quiet>true</quiet>
          <debug>false</debug>
          <doclint>none</doclint>
          <additionalOptions>
            <additionalOption>--add-modules jdk.incubator.vector</additionalOption>
          </additionalOptions>
          <!-- excludePackageNames>edu.rit.*</excludePackageNames -->
        </configuration>
        <inherited>true</inherited>
        <reportSets>
          <reportSet>
            <id>aggregate</id>
            <reports>
              <report>aggregate</report>
              <report>test-aggregate</report>
            </reports>
          </reportSet>
        </reportSets>
        <version>${javadoc.version}</version>
      </plugin>
      <plugin>
        <artifactId>maven-jxr-plugin</artifactId>
        <reportSets>
          <reportSet>
            <id>aggregate</id>
            <reports>
              <report>aggregate</report>
              <report>test-aggregate</report>
            </reports>
          </reportSet>
        </reportSets>
        <configuration>
          <linkJavadoc>true</linkJavadoc>
          <javadocVersion>${compileVersion}</javadocVersion>
        </configuration>
        <version>${jxr.version}</version>
      </plugin>
      <plugin>
        <artifactId>maven-surefire-report-plugin</artifactId>
        <configuration>
          <aggregate>true</aggregate>
          <alwaysGenerateSurefireReport>true</alwaysGenerateSurefireReport>
          <linkXRef>true</linkXRef>
        </configuration>
        <version>${surefire.version}</version>
      </plugin>
      <plugin>
        <artifactId>maven-linkcheck-plugin</artifactId>
        <version>${linkcheck.version}</version>
      </plugin>
      <plugin>
        <artifactId>maven-pmd-plugin</artifactId>
        <configuration>
          <linkXRef>true</linkXRef>
          <minimumPriority>2</minimumPriority>
          <minimumTokens>500</minimumTokens>
          <targetJdk>${targetVersion}</targetJdk>
          <typeResolution>true</typeResolution>
        </configuration>
        <reportSets>
          <reportSet>
            <id>aggregate</id>
            <inherited>false</inherited>
            <reports>
              <report>aggregate-pmd</report>
              <report>aggregate-cpd</report>
            </reports>
          </reportSet>
        </reportSets>
        <version>${pmd.version}</version>
      </plugin>
      <plugin>
        <artifactId>maven-checkstyle-plugin</artifactId>
        <version>${checkstyle.version}</version>
        <configuration>
          <goal>checkstyle-aggregate</goal>
        </configuration>
      </plugin>
    </plugins>
  </reporting>
  <repositories>
    <repository>
      <id>1.ffx.repo</id>
      <name>FFX Dependency Repository</name>
      <releases>
        <checksumPolicy>ignore</checksumPolicy>
        <enabled>true</enabled>
        <updatePolicy>daily</updatePolicy>
      </releases>
      <snapshots>
        <enabled>true</enabled>
      </snapshots>
      <url>https://github.com/mjschnie/dependency/raw/master</url>
    </repository>
    <repository>
      <id>2.apache.repo</id>
      <name>Apache Maven Repository</name>
      <releases>
        <enabled>true</enabled>
      </releases>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
      <url>https://repo.maven.apache.org/maven2</url>
    </repository>
    <repository>
      <id>3.u.manchester.repo</id>
      <name>TornadoVM Repository</name>
      <releases>
        <enabled>true</enabled>
      </releases>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
      <url>https://raw.githubusercontent.com/beehive-lab/tornado/maven-tornadovm</url>
    </repository>
  </repositories>
  <scm>
    <connection>scm:git:https://github.com/SchniedersLab/forcefieldx.git</connection>
    <developerConnection>scm:git:git@github.com:SchniedersLab/forcefieldx.git</developerConnection>
    <url>https://github.com/SchniedersLab/forcefieldx</url>
  </scm>
  <url>https://ffx.biochem.uiowa.edu</url>
  <version>26.0.1</version>
</project>