public diffusion(String filePath, String fileType) {
try {
prefix = filePath.substring(0, (filePath.length() - 4));
System.out.println("Reading file trj_typ: " + prefix);
if (fileType.equals("dcd")) {
DCD = new dcd(filePath);
DCD.openInputStream();
System.out.printf("DCD file %s \n", DCD.read_dcd());
DCD.est_file_length();
DCD.print_header();
DCD.gen_DCD_body_pointers();
} else if (fileType.equals("trr")) {
FR = new FileReader(filePath);
dFile = new BufferedReader(FR);
}
outcrd = new FileWriter(prefix + "_crd.xvg");
doutC = new PrintWriter(outcrd, true);
outvel = new FileWriter(prefix + "_vel.xvg");
doutV = new PrintWriter(outvel, true);
outfrc = new FileWriter(prefix + "_frc.xvg");
doutF = new PrintWriter(outfrc, true);
frameData1 = new String[5];
frameData2 = new String[5];
sumX = sumY = sumZ = 0;
} catch (IOException e) {
System.err.println(e);
}
}
public void read_dcd_file() {
String line;
int lineCount, frameCount, natoms, i, NSET, N;
float time;
lineCount = frameCount = 0;
N = DCD.get_N();
NSET = DCD.get_NSET();
}
public void read_dcd_frame(int n, int nset) {
int i, j;
for (i = 0; i < 3; i++) {
System.out.println(DCD.read_int());
for (j = 0; j < n; j++) {
System.out.println("[" + i + "," + j + "]=" + DCD.read_float());
}
System.out.println(DCD.read_int());
}
}