First commit

pom.xml

@@ -0,0 +1,39 @@
+<?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">
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>ru.lesqm</groupId>
+    <artifactId>TDDFTExcitationEnergiesFormatter</artifactId>
+    <version>0.1-SNAPSHOT</version>
+    <packaging>jar</packaging>
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
+    </properties>
+    <build>
+        <plugins>
+            <plugin>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <mainClass>ru.lesqm.tddftexcitationenergies.formatter.Main</mainClass>
+                        </manifest>
+                    </archive>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>make-assembly</id>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>

src/main/java/ru/lesqm/tddftexcitationenergies/formatter/Main.java

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+package ru.lesqm.tddftexcitationenergies.formatter;
+
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.PrintWriter;
+import ru.lesqm.tddftexcitationenergies.formatter.models.TEERow;
+import java.util.ArrayList;
+import java.util.InputMismatchException;
+import java.util.List;
+import java.util.Locale;
+import java.util.NoSuchElementException;
+import java.util.Scanner;
+import ru.lesqm.tddftexcitationenergies.formatter.models.ExcitedState;
+import ru.lesqm.tddftexcitationenergies.formatter.models.ExcitedStateRow;
+
+public class Main {
+
+    public static void usage() {
+        System.out.println("Usage: format [flags] <input>");
+        System.out.println("    -a    skip rows with % < 10");
+        System.exit(0);
+    }
+
+    public static void main(String[] args) throws FileNotFoundException {
+        if (args.length < 2) {
+            usage();
+        }
+
+        boolean skipLw = false;
+
+        String input = null;
+        for (String a : args) {
+            if (a.startsWith("-a")) {
+                skipLw = true;
+            } else {
+                input = a;
+            }
+        }
+
+        if (input == null) {
+            usage();
+        }
+
+        Scanner s = new Scanner(new FileInputStream(input));
+        s.useLocale(Locale.US);
+
+        String str;
+
+        System.out.print("Searching for 'RESULTS FROM SPIN-ADAPTED ANTISYMMETRIZED PRODUCT (SAPS)' title: ");
+        while (!(str = s.nextLine()).trim().startsWith("RESULTS FROM SPIN-ADAPTED ANTISYMMETRIZED PRODUCT (SAPS)")) {
+        }
+
+        s.nextLine(); // Skip title 2
+        s.nextLine(); // Skip separator line
+        s.nextLine(); // Skip empty line
+
+        System.out.println("done");
+
+        List<ExcitedState> excitedStates = new ArrayList<>();
+
+        int stateNumber = 0;
+        for (; s.hasNextLine(); stateNumber++) {
+
+            System.out.print("Searching for 'EXCITED STATE ' title: ");
+            try {
+                while (!(str = s.nextLine()).trim().startsWith("EXCITED STATE ")) {
+                }
+            } catch (NoSuchElementException e) {
+                break;
+            }
+
+            System.out.println("done");
+
+            String excitedStateString = str;
+
+            s.nextLine(); // Skip empty line
+            s.nextLine(); // Skip separator line
+            s.nextLine(); // Skip header 1
+            s.nextLine(); // Skip header 2
+            s.nextLine(); // Skip separator line
+
+            System.out.print("Parsing 'EXCITED STATE ...'" + "(" + (stateNumber + 1) + "):");
+            ExcitedState excitedState = new ExcitedState();
+
+            while (true) {
+                try {
+                    ExcitedStateRow stateRow = new ExcitedStateRow();
+
+                    stateRow.fromMo = s.nextInt();
+                    stateRow.toMo = s.nextInt();
+                    stateRow.sapCoefficient = s.nextDouble();
+
+                    excitedState.rows.add(stateRow);
+                } catch (NumberFormatException | InputMismatchException e) {
+                    break;
+                }
+            }
+
+            excitedStates.add(excitedState);
+
+            System.out.println("done");
+        }
+        System.out.println("end of file");
+
+        s.close();
+
+        s = new Scanner(new FileInputStream(input));
+        s.useLocale(Locale.US);
+
+        System.out.print("Searching for 'TDDFT EXCITATION ENERGIES' title: ");
+        while (!(str = s.nextLine()).trim().equalsIgnoreCase("TDDFT EXCITATION ENERGIES")) {
+        }
+
+        s.nextLine(); // Skip header
+        s.nextLine(); // Skip separator line
+
+        System.out.println("done");
+
+        System.out.print("Parsing 'TDDFT EXCITATION ENERGIES' table: ");
+        List<TEERow> teeRows = new ArrayList<>();
+        for (int i = 0; i < stateNumber; i++) {
+            TEERow teerow = new TEERow();
+
+            teerow.state = s.next();
+            teerow.hartree = s.nextDouble();
+            teerow.hv = s.nextDouble();
+            teerow.kcalmol = s.nextDouble();
+            teerow.cm1 = s.nextDouble();
+            teerow.nanometers = s.nextDouble();
+            teerow.oscstr = s.nextDouble();
+
+            teeRows.add(teerow);
+        }
+
+        s.close();
+        System.out.println("done");
+
+        System.out.print("Writing result to 'result.out': ");
+
+        PrintWriter pw = new PrintWriter(new FileOutputStream("result.out"));
+
+        for (int i = 0; i < teeRows.size(); i++) {
+            TEERow tee = teeRows.get(i);
+            ExcitedState state = excitedStates.get(i);
+
+            boolean first = true;
+            for (ExcitedStateRow r : state.rows) {
+                if (skipLw && (Math.pow(r.sapCoefficient, 2) * 100) < 10) {
+                    continue;
+                }
+
+                if (first) {
+                    first = false;
+                    pw.format("%s\t%d\t", tee.state, i + 1);
+                } else {
+                    pw.format("\t\t");
+                }
+                pw.format(
+                        "%d\t%d\t%d\t%d\t%f\n",
+                        r.fromMo,
+                        r.toMo,
+                        (int) Math.rint((Math.pow(r.sapCoefficient, 2d) * 100d)),
+                        (int) Math.rint(tee.nanometers),
+                        tee.oscstr);
+            }
+        }
+
+        pw.close();
+        System.out.println("done");
+    }
+
+}

src/main/java/ru/lesqm/tddftexcitationenergies/formatter/models/ExcitedState.java

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+package ru.lesqm.tddftexcitationenergies.formatter.models;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class ExcitedState {
+
+    public int state;
+    public double energy;
+    public double s;
+    public String spaceSym;
+
+    public List<ExcitedStateRow> rows = new ArrayList<>();
+
+    @Override
+    public String toString() {
+        return "ExcitedState{" + "state=" + state + ", energy=" + energy + ", s=" + s + ", spaceSym=" + spaceSym + ", rows=" + rows + '}';
+    }
+
+}

src/main/java/ru/lesqm/tddftexcitationenergies/formatter/models/ExcitedStateRow.java

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+package ru.lesqm.tddftexcitationenergies.formatter.models;
+
+public class ExcitedStateRow {
+
+    public int fromMo;
+    public int toMo;
+    public double sapCoefficient;
+
+    @Override
+    public String toString() {
+        return "ExcitedStateRow{" + "fromMo=" + fromMo + ", toMo=" + toMo + ", sapCoefficient=" + sapCoefficient + '}';
+    }
+
+}

src/main/java/ru/lesqm/tddftexcitationenergies/formatter/models/TEERow.java

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+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package ru.lesqm.tddftexcitationenergies.formatter.models;
+
+/**
+ *
+ * @author User
+ */
+public class TEERow {
+
+    public String state;
+    public double hartree;
+    public double hv;
+    public double kcalmol;
+    public double cm1;
+    public double nanometers;
+    public double oscstr;
+
+    @Override
+    public String toString() {
+        return "TEERow{" + "state=" + state + ", hartree=" + hartree + ", hv=" + hv + ", kcalmol=" + kcalmol + ", cm1=" + cm1 + ", nanometers=" + nanometers + ", oscstr=" + oscstr + '}';
+    }
+
+}