ref + docfix

src/main/java/neqsim/fluidmechanics/flownode/fluidboundary/heatmasstransfercalc/nonequilibriumfluidboundary/NonEquilibriumFluidBoundary.java

@@ -628,8 +628,5 @@ public void solve() {
     } while (Math.abs((oldHeatFlux - heatFlux) / heatFlux) > 1e-6 && heatTransferCalc
         && iterInner < 50);
     init();
-    // System.out.println("iterInner " +iterInner + " temp gas " +
-    // interphaseSystem.getTemperature(0)+ " temp liq " +
-    // interphaseSystem.getTemperature(1));
   }
 }

src/main/java/neqsim/process/equipment/ProcessEquipmentInterface.java

@@ -89,8 +89,7 @@ public default boolean needRecalculation() {
    * setController.
    * </p>
    *
-   * @param controller a {@link neqsim.process.controllerdevice.ControllerDeviceInterface}
-   *        object
+   * @param controller a {@link neqsim.process.controllerdevice.ControllerDeviceInterface} object
    */
   public void setController(ControllerDeviceInterface controller);
 
@@ -166,8 +165,7 @@ public default SystemInterface getFluid() {
    * runConditionAnalysis.
    * </p>
    *
-   * @param refExchanger a
-   *        {@link neqsim.process.equipment.ProcessEquipmentInterface} object
+   * @param refExchanger a {@link neqsim.process.equipment.ProcessEquipmentInterface} object
    */
   public void runConditionAnalysis(ProcessEquipmentInterface refExchanger);
 
@@ -216,10 +214,10 @@ public default SystemInterface getFluid() {
 
   /**
    * <p>
-   * toJson.
+   * Serializes the Process Equipment along with its state to a JSON string.
    * </p>
    *
-   * @return a String
+   * @return json string.
    */
   public String toJson();
 

src/main/java/neqsim/process/equipment/tank/Tank.java

@@ -1,6 +1,8 @@
 package neqsim.process.equipment.tank;
 
 import java.util.UUID;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import neqsim.process.equipment.ProcessEquipmentBaseClass;
 import neqsim.process.equipment.mixer.Mixer;
 import neqsim.process.equipment.stream.Stream;
@@ -20,6 +22,8 @@
 public class Tank extends ProcessEquipmentBaseClass {
   /** Serialization version UID. */
   private static final long serialVersionUID = 1000;
+  /** Logger object for class. */
+  static Logger logger = LogManager.getLogger(Tank.class);
 
   SystemInterface thermoSystem;
   SystemInterface gasSystem;
@@ -148,14 +152,29 @@ public StreamInterface getLiquid() {
     return getLiquidOutStream();
   }
 
-  /** {@inheritDoc} */
+  /**
+   * {@inheritDoc}
+   *
+   * <p>
+   * Calculates the following properties:
+   * <ul>
+   * <li>steelWallTemperature</li>
+   * <li>gasOutStream</li>
+   * <li>liquidOutStream</li>
+   * <li><code>thermoSystem</code> including properties</li>.
+   * <li>liquidLevel</li>
+   * <li>liquidVolume</li>
+   * <li>gasVolume</li>
+   * </ul>
+   * </p>
+   */
   @Override
   public void run(UUID id) {
     inletStreamMixer.run(id);
     SystemInterface thermoSystem2 = inletStreamMixer.getOutletStream().getThermoSystem().clone();
     ThermodynamicOperations ops = new ThermodynamicOperations(thermoSystem2);
     ops.VUflash(thermoSystem2.getVolume(), thermoSystem2.getInternalEnergy());
-    System.out.println("Volume " + thermoSystem2.getVolume() + " internalEnergy "
+    logger.info("Volume " + thermoSystem2.getVolume() + " internalEnergy "
         + thermoSystem2.getInternalEnergy());
     steelWallTemperature = thermoSystem2.getTemperature();
     if (thermoSystem2.hasPhaseType("gas")) {
@@ -172,7 +191,7 @@ public void run(UUID id) {
     thermoSystem = thermoSystem2.clone();
     thermoSystem.setTotalNumberOfMoles(1.0e-10);
     thermoSystem.init(1);
-    System.out.println("number of phases " + thermoSystem.getNumberOfPhases());
+    logger.info("number of phases " + thermoSystem.getNumberOfPhases());
     for (int j = 0; j < thermoSystem.getNumberOfPhases(); j++) {
       double relFact = gasVolume / (thermoSystem.getPhase(j).getVolume() * 1.0e-5);
       if (j == 1) {
@@ -191,10 +210,10 @@ public void run(UUID id) {
       thermoSystem.setBeta(1.0 - 1e-10);
     }
     thermoSystem.init(3);
-    System.out.println("moles in separator " + thermoSystem.getNumberOfMoles());
+    logger.info("moles in separator " + thermoSystem.getNumberOfMoles());
     double volume1 = thermoSystem.getVolume();
-    System.out.println("volume1 bef " + volume1);
-    System.out.println("beta " + thermoSystem.getBeta());
+    logger.info("volume1 bef " + volume1);
+    logger.info("beta " + thermoSystem.getBeta());
 
     if (thermoSystem2.getNumberOfPhases() == 2) {
       liquidLevel = thermoSystem.getPhase(1).getVolume() * 1e-5 / (liquidVolume + gasVolume);
@@ -205,7 +224,7 @@ public void run(UUID id) {
         getLiquidLevel() * 3.14 / 4.0 * separatorDiameter * separatorDiameter * separatorLength;
     gasVolume = (1.0 - getLiquidLevel()) * 3.14 / 4.0 * separatorDiameter * separatorDiameter
         * separatorLength;
-    System.out.println("moles out" + liquidOutStream.getThermoSystem().getTotalNumberOfMoles());
+    logger.info("moles out" + liquidOutStream.getThermoSystem().getTotalNumberOfMoles());
 
     setCalculationIdentifier(id);
   }

src/main/java/neqsim/thermo/component/Component.java

@@ -50,10 +50,11 @@ public abstract class Component implements ComponentInterface {
   /** Mole fraction of Component in Phase. */
   protected double x = 0;
   /**
-   * Number of moles of Component in System. <code>numberOfMoles = totalNumberOfMoles * z</code>.
+   * Number of moles of Component in System. Ideally
+   * <code>numberOfMoles = totalNumberOfMoles * z</code>.
    */
   protected double numberOfMoles = 0.0;
-  /** Number of moles of Component in Phase. <code>totalNumberOfMoles * x * beta</code>. */
+  /** Number of moles of Component in Phase. Ideally <code>totalNumberOfMoles * x * beta</code>. */
   protected double numberOfMolesInPhase = 0.0;
   protected double K;
 

src/main/java/neqsim/thermo/phase/PhaseEos.java

@@ -36,7 +36,7 @@ public abstract class PhaseEos extends Phase implements PhaseEosInterface {
   public double delta1 = 0;
   public double delta2 = 0;
 
-  protected EosMixingRules mixSelect = null;
+  protected EosMixingRules mixSelect = new EosMixingRules();
   protected EosMixingRulesInterface mixRule = null;
   double uEOS = 0;
   double wEOS = 0;
@@ -63,7 +63,6 @@ public PhaseEos clone() {
    * </p>
    */
   public PhaseEos() {
-    mixSelect = new EosMixingRules();
     componentArray = new ComponentEosInterface[ThermodynamicModelSettings.MAX_NUMBER_OF_COMPONENTS];
     mixRule = mixSelect.getMixingRule(1);
     // solver = new newtonRhapson();

src/main/java/neqsim/thermo/phase/PhaseInterface.java

@@ -39,10 +39,10 @@ public interface PhaseInterface extends ThermodynamicConstantsInterface, Cloneab
 
   /**
    * <p>
-   * setMoleFractions.
+   * Set <code>x</code> and normalize for all Components in phase.
    * </p>
    *
-   * @param x an array of type double
+   * @param x Mole fractions of component in a phase.
    */
   public void setMoleFractions(double[] x);
 
@@ -690,8 +690,11 @@ public default void initPhysicalProperties(String name) {
   public double getpH();
 
   /**
+   * Normalize property <code>x</code>.
+   * 
    * <p>
-   * normalize.
+   * Property <code>x</code> is the mole fraction of a component in a specific phase. Normalizing,
+   * means that the sum of <code>x</code> for all Components in a phase equal 1.0.
    * </p>
    */
   public void normalize();
@@ -1280,10 +1283,10 @@ public default void setMixingRule(int mr) {
 
   /**
    * <p>
-   * getNumberOfMolesInPhase.
+   * Get the number of moles the phase contains.
    * </p>
    *
-   * @return a double
+   * @return The number of moles in the phase.
    */
   public double getNumberOfMolesInPhase();
 
@@ -1723,7 +1726,7 @@ public default void setMixingRule(int mr) {
 
   /**
    * <p>
-   * dFdT.
+   * Calculate derivative of F per Temperature, i.e., dF/dT.
    * </p>
    *
    * @return a double
@@ -1732,7 +1735,7 @@ public default void setMixingRule(int mr) {
 
   /**
    * <p>
-   * dFdV.
+   * Calculate derivative of F per Volume, i.e., dF/dV.
    * </p>
    *
    * @return a double
@@ -1741,7 +1744,7 @@ public default void setMixingRule(int mr) {
 
   /**
    * <p>
-   * dFdTdV.
+   * Calculate derivative of F per Temperature and Volume, i.e., dF/dT * 1/dV.
    * </p>
    *
    * @return a double
@@ -1818,8 +1821,8 @@ public default void setMixingRule(int mr) {
   public double getLogInfiniteDiluteFugacity(int k);
 
   /**
-   * Get mixing rule
-   * 
+   * Get mixing rule.
+   *
    * @return a MixingRulesInterface
    */
   public MixingRulesInterface getMixingRule();

src/main/java/neqsim/thermo/system/SystemInterface.java

@@ -1472,7 +1472,7 @@ public default int getPhaseNumberOfPhase(String phaseTypeName) {
 
   /**
    * <p>
-   * Getter for property <code>TC</code>.
+   * Get critical temperature.
    * </p>
    *
    * @return Critical temperature
@@ -1488,13 +1488,14 @@ public default int getPhaseNumberOfPhase(String phaseTypeName) {
 
   /**
    * <p>
-   * method to return temperature.
+   * method to return temperature from a specific phase.
    * </p>
    *
    * @param phaseNumber phase to get temperature of
    * @return temperature in unit Kelvin
    */
-  public double getTemperature(int phaseNumber);
+  public double getTemperature(int phaseNumber); // TODO: is it possible for the phases to have
+                                                 // different temperatures?
 
   /**
    * method to return temperature in a specified unit.
@@ -2119,9 +2120,10 @@ public default void prettyPrint() {
   public void setAttractiveTerm(int i);
 
   /**
+   * Setter for property <code>beta</code>.
    * <p>
-   * Setter for property <code>beta</code>. NB! Sets beta = b for first phase and 1-b for second
-   * phase, not for multiphase systems.
+   * NB! Sets beta = b for first (heaviest) phase and 1-b for second (lightest) phase, not for
+   * multiphase systems.
    * </p>
    *
    * @param b Beta value to set.

src/main/java/neqsim/thermo/util/readwrite/EclipseFluidReadWrite.java

@@ -371,7 +371,6 @@ public static SystemInterface read(String inputFile) {
         }
       }
 
-      // System.out.println(st);
       fluid.setMixingRule(2);
       fluid.useVolumeCorrection(true);
       fluid.init(0);
@@ -385,8 +384,6 @@ public static SystemInterface read(String inputFile) {
           }
         }
       }
-
-      // fluid.display();
     } catch (Exception ex) {
       logger.error(ex.getMessage(), ex);
     }

src/main/java/neqsim/thermodynamicoperations/ThermodynamicOperations.java

@@ -140,7 +140,7 @@ public void TPSolidflash() {
   }
 
   /**
-   * Method to perform a flash at given temperature, pressure and specified volume The number of
+   * Method to perform a flash at given temperature, pressure and specified volume. The number of
    * moles in the system are changed to match the specified volume.
    *
    * @param volumeSpec is the specified volume
@@ -1380,6 +1380,7 @@ public void constantPhaseFractionTemperatureFlash(double fraction) throws IsNaNE
       fraction = 1.0 - 1.0e-10;
     }
     ConstantDutyFlashInterface operation = new ConstantDutyTemperatureFlash(system);
+    // TODO: bug, sum of beta will not equal 1
     system.setBeta(1, fraction);
     system.setBeta(0, fraction);
     operation.run();

src/test/java/neqsim/process/measurementdevice/nmVOCTest.java

@@ -121,7 +121,7 @@ public void testGetTotalFlowRate() {
   }
 
   @Test
-  public void nmVOCFlowRateTest() {
+  public void testnmVOCFlowRate() {
     process1.run();
     Assertions.assertEquals(vocanalyser1.getMeasuredValue(), 10555.540704);
     Assertions.assertEquals(vocanalyser1.getMeasuredValue("tonnes/year"), 10555.540704);

src/test/java/neqsim/process/processmodel/LargeCombinedModelsTest.java

@@ -538,7 +538,7 @@ public ProcessSystem createExpanderProcessModel(Separator dewPointScrubber2,
   }
 
   @Test
-  public void tesExpanderProcess() {
+  public void testExpanderProcess() {
     // wellFluid.setMultiPhaseCheck(true);
     ProcessSystem wellprocess = getWellStreamAndManifoldModel(wellFluid);
     wellprocess.run();

src/test/java/neqsim/process/processmodel/SalesGasAndStableOilTest.java

@@ -2,6 +2,7 @@
 
 import java.io.File;
 import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import neqsim.process.equipment.compressor.Compressor;
 import neqsim.process.equipment.expander.Expander;
@@ -20,13 +21,11 @@ public class SalesGasAndStableOilTest extends neqsim.NeqSimTest {
   File file = new File("src/test/java/neqsim/process/processmodel");
   String fileFluid1 = file.getAbsolutePath() + "/feedfluid.e300";
 
+  @Disabled("No assertions")
   @Test
   public void testProcess() {
     SystemInterface wellFluid = neqsim.thermo.util.readwrite.EclipseFluidReadWrite.read(fileFluid1);
     // wellFluid.setMultiPhaseCheck(true);
-
-    neqsim.process.equipment.stream.Stream wellStream =
-        new neqsim.process.equipment.stream.Stream("HP well stream", wellFluid);
     SystemInterface LPwellFLuid = wellFluid.clone();
 
     Stream wellStreamHP = new neqsim.process.equipment.stream.Stream("HP well stream", wellFluid);