private void read_Array(float[][] arr, int r) {
try {
int i, j, tkns;
String[] tempArr;
String line, temp;
StringTokenizer token;
for (i = 0;
i < r;
i++) { // Turn this for loop into a function because it will be reused 3 times.
line = dFile.readLine();
token = new StringTokenizer(line);
tkns = token.countTokens();
if (tkns == 4) {
temp = token.nextToken();
tempArr = token.nextToken().split("\\]|=|\\{|,");
arr[i][0] = Float.parseFloat(tempArr[3]);
tempArr = token.nextToken().split(",");
arr[i][1] = Float.parseFloat(tempArr[0]);
tempArr = token.nextToken().split("\\}");
arr[i][2] = Float.parseFloat(tempArr[0]);
} else if (tkns == 5) {
temp = token.nextToken();
temp = token.nextToken();
tempArr = token.nextToken().split("\\]|=|\\{|,");
arr[i][0] = Float.parseFloat(tempArr[0]);
tempArr = token.nextToken().split(",");
arr[i][1] = Float.parseFloat(tempArr[0]);
tempArr = token.nextToken().split("\\}");
arr[i][2] = Float.parseFloat(tempArr[0]);
}
}
} catch (IOException e) {
System.err.println(e);
}
}
// private float mean(int nO){return 0.0;}
private void read_header(String line, String[] frameData) {
try {
String[] tempArr;
String temp;
StringTokenizer token;
token = new StringTokenizer(line);
int c, r, i, j, tkns;
if (token.countTokens() != 3) {
System.out.println(
"ERROR:A line that does not have 3 tokens can not be the begining of a frame.");
} else {
temp = token.nextToken();
temp = token.nextToken();
tempArr = token.nextToken().split(":");
frameData[0] = tempArr[0];
line = dFile.readLine();
token = new StringTokenizer(line);
temp = token.nextToken();
frameData[1] = token.nextToken();
temp = token.nextToken();
frameData[2] = token.nextToken();
tempArr = token.nextToken().split("=");
frameData[3] = tempArr[1];
temp = token.nextToken();
frameData[4] = token.nextToken();
}
} catch (IOException e) {
System.err.println(e);
}
}
private void read_frame(float[][] box, float[][] crd, float[][] vel, float[][] frc) {
try {
String[] tempArr;
String line, temp;
StringTokenizer token;
int c, r, i, j, tkns;
line = dFile.readLine();
token = new StringTokenizer(line);
if (token.nextToken().equals("box")) {
tempArr = token.nextToken().split("\\(|x|\\)|:");
r = Integer.parseInt(tempArr[1]);
c = Integer.parseInt(tempArr[2]);
read_Array(box, r);
}
line = dFile.readLine();
token = new StringTokenizer(line);
if (token.nextToken().equals("x")) {
tempArr = token.nextToken().split("\\(|x|\\)|:");
r = Integer.parseInt(tempArr[1]);
c = Integer.parseInt(tempArr[2]);
read_Array(crd, r);
}
line = dFile.readLine();
token = new StringTokenizer(line);
if (token.nextToken().equals("v")) {
tempArr = token.nextToken().split("\\(|x|\\)|:");
r = Integer.parseInt(tempArr[1]);
c = Integer.parseInt(tempArr[2]);
read_Array(vel, r);
}
line = dFile.readLine();
token = new StringTokenizer(line);
if (token.nextToken().equals("f")) {
tempArr = token.nextToken().split("\\(|x|\\)|:");
r = Integer.parseInt(tempArr[1]);
c = Integer.parseInt(tempArr[2]);
read_Array(frc, r);
}
} catch (IOException e) {
System.err.println(e);
}
}
public void read_trr_file() {
try {
String line;
int lineCount, frameCount, natoms, i;
float time;
lineCount = frameCount = 0;
while ((line = dFile.readLine()) != null) {
if (frameCount == 0) {
read_header(line, frameData1);
natoms = Integer.parseInt(frameData1[1]);
box1 = new float[3][3];
crd1 = new float[natoms][3];
vel1 = new float[natoms][3];
frc1 = new float[natoms][3];
read_frame(box1, crd1, vel1, frc1);
frameCount++;
} else if (frameCount == 1) {
read_header(line, frameData2);
natoms = Integer.parseInt(frameData2[1]);
time = Float.parseFloat(frameData2[3]);
box2 = new float[3][3];
crd2 = new float[natoms][3];
vel2 = new float[natoms][3];
frc2 = new float[natoms][3];
read_frame(box2, crd2, vel2, frc2);
write_xvg_mean_sd(time, natoms, crd1, crd2, box2, "crd");
write_MSD(time, natoms, crd1, crd2, box2);
write_xvg_mean_sd(time, natoms, vel1, vel2, box2, "vel");
write_xvg_mean_sd(time, natoms, frc1, frc2, box2, "frc");
// System.out.println(frameCount+" "+time+" crd1, crd2: "+frameData1[1]+"
// "+frameData2[1]+" "+frameData1[2]+" "+frameData2[2]+" "+frameData1[3]+"
// "+frameData2[3]);
frameCount++;
} else {
if ((frameCount % 2) == 0) {
read_header(line, frameData1);
natoms = Integer.parseInt(frameData1[1]);
time = Float.parseFloat(frameData1[3]);
box1 = new float[3][3];
crd1 = new float[natoms][3];
vel1 = new float[natoms][3];
frc1 = new float[natoms][3];
read_frame(box1, crd1, vel1, frc1);
write_xvg_mean_sd(time, natoms, crd2, crd1, box1, "crd");
write_xvg_mean_sd(time, natoms, vel2, vel1, box1, "vel");
write_xvg_mean_sd(time, natoms, frc2, frc1, box1, "frc");
// System.out.println(frameCount+" "+time+" crd2, crd1: "+frameData2[1]+"
// "+frameData1[1]+" "+frameData2[2]+" "+frameData1[2]+" "+frameData2[3]+"
// "+frameData1[3]);
frameCount++;
} else {
read_header(line, frameData2);
natoms = Integer.parseInt(frameData2[1]);
time = Float.parseFloat(frameData2[3]);
box2 = new float[3][3];
crd2 = new float[natoms][3];
vel2 = new float[natoms][3];
frc2 = new float[natoms][3];
read_frame(box2, crd2, vel2, frc2);
write_xvg_mean_sd(time, natoms, crd1, crd2, box2, "crd");
write_xvg_mean_sd(time, natoms, vel1, vel2, box2, "vel");
write_xvg_mean_sd(time, natoms, frc1, frc2, box2, "frc");
// System.out.println(frameCount+" "+time+" crd1, crd2: "+frameData1[1]+"
// "+frameData2[1]+" "+frameData1[2]+" "+frameData2[2]+" "+frameData1[3]+"
// "+frameData2[3]);
frameCount++;
}
}
}
} catch (IOException e) {
System.err.println(e);
}
}