I am writing a code to read in large .xyz files. These type of files are useful for Molecular Dynamics visualizers like VMD. So the file format looks something like this
#Number of particles
#frame number
#Coordinates
As an example:
5
0
C 1.23 2.33 4.56
C 1.23 2.33 5.56
C 1.23 2.33 6.56
C 1.23 2.33 7.56
C 1.23 2.33 8.56
5
1
C 2.23 2.33 4.56
C 2.23 3.33 5.56
C 2.23 4.33 6.56
C 2.23 5.33 7.56
C 2.23 6.33 8.56
and so on. I was trying to understand this post here https://codereview.stackexchange.com/questions/201743/processing-xyz-data-from-a-large-file which talks about efficiently reading from large datasets using operator overloading method. I am trying to write a class which can read such large trajectory files and give me the following outputs : 1) number of particles 2) Total number of frames 3)set of Coordinates at each time step. So i have tried to write down the following based on this post to read in the the file format as mentioned above. So far the code below is able to read a single frame and exits after that.
#include <iostream>
#include <vector>
#include <fstream>
struct Particle{
long double x,y,z;
char tab ='\t';
char newline = '\n';
char atom ;
friend std::istream& operator>>(std::istream& in, Particle &xyz) {
in >> xyz.atom >> xyz.x >> xyz.y >> xyz.z ;
return in;
}
friend std::ostream& operator<<(std::ostream& out, Particle &xyz){
out << xyz.x << xyz.tab << xyz.y << xyz.tab << xyz.z << xyz.newline;
return out;
}
};
class XYZ_frame_read
{
int curr_frame;
int num_particles;
std::vector<Particle> coordinates_t;
public:
friend std::istream& operator>>(std::istream& in, XYZ_frame_read &traj ){
in >> traj.num_particles;
in >> traj.curr_frame;
Particle p;
while(in >> p){
traj.coordinates_t.push_back(p);
}
return in;
}
friend std::ostream& operator<<(std::ostream& out, XYZ_frame_read &traj){
for(int i = 0; i< traj.num_particles ;i ++){
out << traj.coordinates_t.at(i) ;
}
return out;
}
};
int main(int argc, char *argv[]){
std::ifstream in(argv[1]);
XYZ_frame_read* frames = new XYZ_frame_read[3];
in >> frames[0];
std::cout << frames[0];
return 0;
}
The problem is I don't understand how will I will implement this method to read the next frames and keep appending them to the coordinates_t vector for each instance of the object XYZ_frame_read. I think I understand how this works so obviously a while(!in.eof()) is out of question, since it'll just read the first frame over and over again. I am a newbie to c++ and am working on a Molecular dyanamics related project, any changes/suggestions are welcome!! Thank you for the help!
EDIT
I have tried using
size_t i = 0;
while(in >> frames[i]){
std::cout << frames[i];
if(i == 3){
break;
}
i++;
}
It returns blank. It doesn't work. The loop doesn't even get executed.
while(!in.eof()) is out of the question because eof doesn't work like that.
Why is iostream::eof inside a loop condition (i.e. `while (!stream.eof())`) considered wrong?
I'm not sure I see the problem, what's wrong with
size_t i = 0;
while (in >> frames[i])
++i;
(apart from the possibility of array bounds errors).
EDIT
This code is incorrect
friend std::istream& operator>>(std::istream& in, XYZ_frame_read &traj) {
in >> traj.num_particles;
in >> traj.curr_frame;
Particle p;
while(in >> p){
traj.coordinates_t.push_back(p);
}
return in;
}
This says keep reading particles until a read fails. That's incorrect, you know how many particles there are. It should say keep reading particles until you have read num_particles of them (or a read fails). I.e. it should say
friend std::istream& operator>>(std::istream& in, XYZ_frame_read &traj) {
in >> traj.num_particles;
in >> traj.curr_frame;
Particle p;
for (int i = 0; i < traj.num_particles && in >> p; ++i)
traj.coordinates_t.push_back(p);
}
return in;
}