Init stuff (#1193)

refact: simplify
test: exclude main functions from jacoco

src/main/java/neqsim/fluidmechanics/flownode/FlowNode.java

@@ -282,10 +282,7 @@ public FlowNode clone() {
   /** {@inheritDoc} */
   @Override
   public void init() {
-    bulkSystem.initBeta();
-    bulkSystem.init_x_y();
-    bulkSystem.init(3);
-    bulkSystem.initPhysicalProperties();
+    initBulkSystem();
   }
 
   /** {@inheritDoc} */

src/main/java/neqsim/fluidmechanics/flownode/FlowNodeInterface.java

@@ -51,6 +51,13 @@ public interface FlowNodeInterface extends Cloneable {
    */
   public void init();
 
+  /**
+   * <p>
+   * initBulkSystem.
+   * </p>
+   */
+  public void initBulkSystem();
+
   /**
    * <p>
    * getVelocity.
@@ -700,13 +707,6 @@ public default void setVelocityIn(DoubleCloneable vel) {
   // public double calcdVoiddz();
   // public double[] calcdxdz();
 
-  /**
-   * <p>
-   * initBulkSystem.
-   * </p>
-   */
-  public void initBulkSystem();
-
   /**
    * <p>
    * display.

src/main/java/neqsim/fluidmechanics/flownode/fluidboundary/heatmasstransfercalc/FluidBoundary.java

@@ -173,7 +173,7 @@ public void initHeatTransferCalc() {}
 
   /**
    * <p>
-   * init.
+   * init. Calls interphaseSystem.init(3)
    * </p>
    */
   public void init() {

src/main/java/neqsim/fluidmechanics/flownode/twophasenode/twophasepipeflownode/DropletFlowNode.java

@@ -151,6 +151,7 @@ public FlowNodeInterface getNextNode() {
    * @param args an array of {@link java.lang.String} objects
    */
   @SuppressWarnings("unused")
+  @ExcludeFromJacocoGeneratedReport
   public static void mainOld(String[] args) {
     SystemInterface testSystem = new SystemSrkCPAstatoil(273.15 + 11.0, 60.0);
     // SystemInterface testSystem = new SystemSrkCPAstatoil(275.3,

src/main/java/neqsim/physicalproperties/interfaceproperties/solidadsorption/PotentialTheoryAdsorption.java

@@ -67,18 +67,20 @@ public void setSolidMaterial(String solidM) {
   public void calcAdsorption(int phaseNum) {
     SystemInterface tempSystem = system.clone();
     tempSystem.init(3);
-    double[] bulkFug = new double[system.getPhase(phaseNum).getNumberOfComponents()];
-    double[] corrx = new double[system.getPhase(phaseNum).getNumberOfComponents()];
-    surfaceExcess = new double[system.getPhase(phaseNum).getNumberOfComponents()];
-    surfaceExcessMolFraction = new double[system.getPhase(phaseNum).getNumberOfComponents()];
+    int numComp = system.getPhase(phaseNum).getNumberOfComponents();
 
-    eps0 = new double[system.getPhase(phaseNum).getNumberOfComponents()];
-    z0 = new double[system.getPhase(phaseNum).getNumberOfComponents()];
-    beta = new double[system.getPhase(phaseNum).getNumberOfComponents()];
+    surfaceExcess = new double[numComp];
+    surfaceExcessMolFraction = new double[numComp];
+
+    eps0 = new double[numComp];
+    z0 = new double[numComp];
+    beta = new double[numComp];
 
     readDBParameters();
 
-    for (int comp = 0; comp < system.getPhase(phaseNum).getNumberOfComponents(); comp++) {
+    double[] bulkFug = new double[numComp];
+    double[] corrx = new double[numComp];
+    for (int comp = 0; comp < numComp; comp++) {
       bulkFug[comp] = system.getPhase(phaseNum).getComponent(comp).getx()
           * system.getPhase(phaseNum).getComponent(comp).getFugacityCoefficient()
           * system.getPhase(phaseNum).getPressure();
@@ -98,7 +100,7 @@ public void calcAdsorption(int phaseNum) {
         iter++;
         sumx = 0.0;
         pressure = 0.0;
-        for (int comp = 0; comp < system.getPhase(phaseNum).getNumberOfComponents(); comp++) {
+        for (int comp = 0; comp < numComp; comp++) {
           double correction =
               Math.exp(epsField[comp][i] / R / system.getPhase(phaseNum).getTemperature());
           fugacityField[comp][i] = correction * bulkFug[comp];
@@ -108,7 +110,7 @@ public void calcAdsorption(int phaseNum) {
           pressure += fugacityField[comp][i]
               / tempSystem.getPhase(phaseNum).getComponent(comp).getFugacityCoefficient();
         }
-        for (int comp = 0; comp < system.getPhase(phaseNum).getNumberOfComponents(); comp++) {
+        for (int comp = 0; comp < numComp; comp++) {
           tempSystem.getPhase(phaseNum).getComponent(comp).setx(corrx[comp]);
           sumx += corrx[comp];
         }
@@ -120,7 +122,7 @@ public void calcAdsorption(int phaseNum) {
         // Math.abs(sumx - 1.0));
       } while (Math.abs(sumx - 1.0) > 1e-12 && iter < 100);
 
-      for (int comp = 0; comp < system.getPhase(phaseNum).getNumberOfComponents(); comp++) {
+      for (int comp = 0; comp < numComp; comp++) {
         surfaceExcess[comp] +=
             deltaz[comp] * (1.0e5 / tempSystem.getPhase(phaseNum).getMolarVolume()
                 * tempSystem.getPhase(phaseNum).getComponent(comp).getx()
@@ -130,10 +132,10 @@ public void calcAdsorption(int phaseNum) {
     }
 
     totalSurfaceExcess = 0.0;
-    for (int comp = 0; comp < system.getPhase(phaseNum).getNumberOfComponents(); comp++) {
+    for (int comp = 0; comp < numComp; comp++) {
       totalSurfaceExcess += surfaceExcess[comp];
     }
-    for (int comp = 0; comp < system.getPhase(phaseNum).getNumberOfComponents(); comp++) {
+    for (int comp = 0; comp < numComp; comp++) {
       surfaceExcessMolFraction[comp] = surfaceExcess[comp] / totalSurfaceExcess;
       // logger.info("surface excess molfrac " + surfaceExcessMolFraction[comp] + "
       // mol/kg adsorbent " + surfaceExcess[comp]);

src/main/java/neqsim/physicalproperties/interfaceproperties/surfacetension/GTSurfaceTensionSimple.java

@@ -193,7 +193,6 @@ public double calcSurfaceTension(int interface1, int interface2) {
         }
         del_den_interface_old[i] = 0;
       }
-      double interact = 1.0;
       double err = 1.0;
       int iterations = 0;
       while (err > 1e-15 && iterations < 1200) {
@@ -277,6 +276,7 @@ public double calcSurfaceTension(int interface1, int interface2) {
       double kappa = 0.0;
       double kappai = 0.0;
       double kappak = 0.0;
+      double interact = 1.0;
       for (int i = 0; i < localSystem.getPhase(0).getNumberOfComponents(); i++) {
         double infli = influenceParam[i];
         // localSystem.getPhase(0).getComponent(i).getSurfaceTenisionInfluenceParameter(localSystem.getPhase(0).getTemperature());

src/main/java/neqsim/pvtsimulation/simulation/SaturationPressure.java

@@ -2,6 +2,7 @@
 
 import neqsim.thermo.system.SystemInterface;
 import neqsim.thermo.system.SystemSrkEos;
+import neqsim.util.ExcludeFromJacocoGeneratedReport;
 
 /**
  * <p>
@@ -91,6 +92,7 @@ public void run() {
    *
    * @param args an array of {@link java.lang.String} objects
    */
+  @ExcludeFromJacocoGeneratedReport
   public static void main(String[] args) {
     // SystemInterface tempSystem = new SystemSrkCPAstatoil(273.15 + 120, 100.0);
     SystemInterface tempSystem = new SystemSrkEos(273.15 + 120, 100.0);

src/main/java/neqsim/pvtsimulation/simulation/SaturationTemperature.java

@@ -2,6 +2,7 @@
 
 import neqsim.thermo.system.SystemInterface;
 import neqsim.thermo.system.SystemSrkEos;
+import neqsim.util.ExcludeFromJacocoGeneratedReport;
 
 /**
  * <p>
@@ -81,6 +82,7 @@ public void run() {
    *
    * @param args an array of {@link java.lang.String} objects
    */
+  @ExcludeFromJacocoGeneratedReport
   public static void main(String[] args) {
     SystemInterface tempSystem = new SystemSrkEos(273.15 + 20, 60.0);
     tempSystem.addComponent("nitrogen", 0.34);

src/main/java/neqsim/pvtsimulation/simulation/SeparatorTest.java

@@ -6,6 +6,7 @@
 import neqsim.thermo.phase.PhaseType;
 import neqsim.thermo.system.SystemInterface;
 import neqsim.thermo.system.SystemSrkEos;
+import neqsim.util.ExcludeFromJacocoGeneratedReport;
 
 /**
  * <p>
@@ -100,6 +101,7 @@ && getThermoSystem().getPhase(0).getType() == PhaseType.GAS) {
    *
    * @param args an array of {@link java.lang.String} objects
    */
+  @ExcludeFromJacocoGeneratedReport
   public static void main(String[] args) {
     SystemInterface tempSystem = new SystemSrkEos(298.0, 300.0);
     tempSystem.addComponent("nitrogen", 0.64);

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

@@ -63,7 +63,7 @@ public abstract class Component implements ComponentInterface {
   protected double bCPA = 0.0;
   protected double mCPA = 0.0;
   protected double srkacentricFactor = 0.0;
-  // TODO: what are the available options here?
+  // TODO: what are the available options here? Can also see solute
   protected String referenceStateType = "solvent";
   protected String associationScheme = "0";
   protected String antoineLiqVapPresType = null;

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

@@ -74,12 +74,12 @@ public ComponentBWRS(String name, double moles, double molesInPhase, int compInd
    * Constructor for ComponentBWRS.
    * </p>
    *
-   * @param number a int
-   * @param TC a double
-   * @param PC a double
-   * @param M a double
-   * @param a a double
-   * @param moles a double
+   * @param number a int. Not used.
+   * @param TC Critical temperature
+   * @param PC Critical pressure
+   * @param M Molar mass
+   * @param a Acentric factor
+   * @param moles Total number of moles of component.
    */
   public ComponentBWRS(int number, double TC, double PC, double M, double a, double moles) {
     super(number, TC, PC, M, a, moles);

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

@@ -37,12 +37,12 @@ public ComponentCSPsrk(String name, double moles, double molesInPhase, int compI
    * Constructor for ComponentCSPsrk.
    * </p>
    *
-   * @param number a int
-   * @param TC a double
-   * @param PC a double
-   * @param M a double
-   * @param a a double
-   * @param moles a double
+   * @param number a int. Not used.
+   * @param TC Critical temperature
+   * @param PC Critical pressure
+   * @param M Molar mass
+   * @param a Acentric factor
+   * @param moles Total number of moles of component.
    */
   public ComponentCSPsrk(int number, double TC, double PC, double M, double a, double moles) {
     super(number, TC, PC, M, a, moles);

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

@@ -58,6 +58,7 @@ public ComponentDesmukhMather(String name, double moles, double molesInPhase, in
   public double getGamma(PhaseInterface phase, int numberOfComponents, double temperature,
       double pressure, PhaseType pt, double[][] HValpha, double[][] HVgij, double[][] intparam,
       String[][] mixRule) {
+    // todo: not actually implemented
     return getGamma(phase, numberOfComponents, temperature, pressure, pt);
   }
 

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

@@ -67,12 +67,12 @@ public ComponentElectrolyteCPA(String name, double moles, double molesInPhase, i
    * Constructor for ComponentElectrolyteCPA.
    * </p>
    *
-   * @param number a int
-   * @param TC a double
-   * @param PC a double
-   * @param M a double
-   * @param a a double
-   * @param moles a double
+   * @param number a int. Not used.
+   * @param TC Critical temperature
+   * @param PC Critical pressure
+   * @param M Molar mass
+   * @param a Acentric factor
+   * @param moles Total number of moles of component.
    */
   public ComponentElectrolyteCPA(int number, double TC, double PC, double M, double a,
       double moles) {

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

@@ -65,12 +65,12 @@ public ComponentElectrolyteCPAOld(String name, double moles, double molesInPhase
    * Constructor for ComponentElectrolyteCPAOld.
    * </p>
    *
-   * @param number a int
-   * @param TC a double
-   * @param PC a double
-   * @param M a double
-   * @param a a double
-   * @param moles a double
+   * @param number a int. Not used.
+   * @param TC Critical temperature
+   * @param PC Critical pressure
+   * @param M Molar mass
+   * @param a Acentric factor
+   * @param moles Total number of moles of component.
    */
   public ComponentElectrolyteCPAOld(int number, double TC, double PC, double M, double a,
       double moles) {

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

@@ -33,12 +33,12 @@ public ComponentElectrolyteCPAstatoil(String name, double moles, double molesInP
    * Constructor for ComponentElectrolyteCPAstatoil.
    * </p>
    *
-   * @param number a int
-   * @param TC a double
-   * @param PC a double
-   * @param M a double
-   * @param a a double
-   * @param moles a double
+   * @param number a int. Not used.
+   * @param TC Critical temperature
+   * @param PC Critical pressure
+   * @param M Molar mass
+   * @param a Acentric factor
+   * @param moles Total number of moles of component.
    */
   public ComponentElectrolyteCPAstatoil(int number, double TC, double PC, double M, double a,
       double moles) {

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

@@ -104,12 +104,12 @@ public ComponentEos(String name, double moles, double molesInPhase, int compInde
    * Constructor for ComponentEos.
    * </p>
    *
-   * @param number a int
+   * @param number a int. Not used.
    * @param TC Critical temperature
    * @param PC Critical pressure
    * @param M Molar mass
    * @param a Acentric factor
-   * @param moles Number of moles
+   * @param moles Total number of moles of component.
    */
   public ComponentEos(int number, double TC, double PC, double M, double a, double moles) {
     super(number, TC, PC, M, a, moles);

src/main/java/neqsim/thermo/component/ComponentGERG2004.java

@@ -32,12 +32,12 @@ public ComponentGERG2004(String name, double moles, double molesInPhase, int com
    * Constructor for ComponentGERG2004.
    * </p>
    *
-   * @param number a int
+   * @param number a int. Not used.
    * @param TC Critical temperature
    * @param PC Critical pressure
    * @param M Molar mass
    * @param a Acentric factor
-   * @param moles Number of moles
+   * @param moles Total number of moles of component.
    */
   public ComponentGERG2004(int number, double TC, double PC, double M, double a, double moles) {
     super(number, TC, PC, M, a, moles);

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

@@ -82,7 +82,6 @@ public double getGamma(PhaseInterface phase, int numberOfComponents, double temp
    */
   public double getGammaNRTL(PhaseInterface phase, int numberOfComponents, double temperature,
       double pressure, PhaseType pt, double[][] HValpha, double[][] HVgij) {
-    double type = phase.getInitType();
     // double ny = 0, Djj = 0, Dii = 0, gij = 0, gjj = 0, gji = 0, gii = 0, F2T = 0, tot2 = 0;
     double A = 0;
     double B = 0;
@@ -237,7 +236,7 @@ public double getGammaNRTL(PhaseInterface phase, int numberOfComponents, double
     gamma = Math.exp(lngamma);
     // System.out.println("gamma " +gamma);
     // if derivates....
-    if (type == 3) {
+    if (phase.getInitType() == 3) {
       double dAdn = 0;
       double dBdn = 0;
       double Etemp = 0;