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Refactor PotentialFileReader

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This commit is contained in:
Richard Berger
2020-06-02 14:18:11 -04:00
parent 60f17e7397
commit 24a0933e2a
4 changed files with 278 additions and 81 deletions
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152
src/potential_file_reader.cpp
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@ -22,6 +22,7 @@
#include "potential_file_reader.h"
#include "utils.h"
#include "tokenizer.h"
#include "fmt/format.h"
#include <cstring>
@ -30,102 +31,111 @@ using namespace LAMMPS_NS;
PotentialFileReader::PotentialFileReader(LAMMPS *lmp,
const std::string &filename,
const std::string &potential_name) :
Pointers(lmp), filename(filename), potential_name(potential_name)
Pointers(lmp),
reader(nullptr),
filename(filename),
potential_name(potential_name)
{
if (comm->me != 0) {
error->one(FLERR, "PotentialFileReader should only be called by proc 0!");
}
fp = force->open_potential(filename.c_str());
if (fp == NULL) {
char str[128];
snprintf(str, 128, "cannot open %s potential file %s", potential_name.c_str(), filename.c_str());
error->one(FLERR, str);
try {
reader = open_potential(filename);
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
}
PotentialFileReader::~PotentialFileReader() {
fclose(fp);
delete reader;
}
void PotentialFileReader::skip_line() {
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
char str[128];
snprintf(str, 128, "Missing line in %s potential file!", potential_name.c_str());
error->one(FLERR, str);
try {
reader->skip_line();
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
}
char *PotentialFileReader::next_line(int nparams) {
// concatenate lines until have nparams words
int n = 0;
int nwords = 0;
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
try {
return reader->next_line(nparams);
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
return nullptr;
}
// strip comment
if ((ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords > 0) {
n = strlen(line);
}
while(nwords == 0 || nwords < nparams) {
char *ptr = fgets(&line[n], MAXLINE - n, fp);
if (ptr == nullptr) {
// EOF
if (nwords > 0 && nwords < nparams) {
char str[128];
snprintf(str, 128, "Incorrect format in %s potential file! %d/%d parameters", potential_name.c_str(), nwords, nparams);
error->one(FLERR, str);
}
return nullptr;
}
// strip comment
if ((ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
// skip line if blank
if (nwords > 0) {
n = strlen(line);
}
}
return line;
}
void PotentialFileReader::next_dvector(int n, double * list) {
int i = 0;
while (i < n) {
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
if (i < n) {
char str[128];
snprintf(str, 128, "Incorrect format in %s potential file! %d/%d values", potential_name.c_str(), i, n);
error->one(FLERR, str);
try {
return reader->next_dvector(n, list);
} catch (FileReaderException & e) {
error->one(FLERR, e.what());
}
}
/* ----------------------------------------------------------------------
open a potential file as specified by name
if fails, search in dir specified by env variable LAMMPS_POTENTIALS
------------------------------------------------------------------------- */
TextFileReader * PotentialFileReader::open_potential(const std::string& path) {
// attempt to open file directly
// if successful, return filename
std::string filepath = path;
std::string filename = utils::path_basename(path);
std::string date;
if(utils::file_is_readable(filepath)) {
date = get_potential_date(filepath);
} else {
// try the environment variable directory
const char *path = getenv("LAMMPS_POTENTIALS");
if (path != nullptr){
std::string pot = utils::path_basename(filepath);
filepath = utils::path_join(path, pot);
if (utils::file_is_readable(filepath)) {
date = get_potential_date(filepath);
} else {
return nullptr;
}
} else {
return nullptr;
}
}
if(!date.empty()) {
utils::logmesg(lmp, fmt::format("Reading potential file {} with DATE: {}", filename, date));
}
return new TextFileReader(filepath, potential_name + " potential");
}
/* ----------------------------------------------------------------------
read first line of potential file
if has DATE field, print following word
------------------------------------------------------------------------- */
std::string PotentialFileReader::get_potential_date(const std::string & path) {
TextFileReader reader(path, potential_name + " potential");
reader.ignore_comments = false;
char * line = nullptr;
while (line = reader.next_line()) {
ValueTokenizer values(line);
while (values.has_next()) {
list[i++] = values.next_double();
std::string word = values.next_string();
if (word == "DATE:") {
if (values.has_next()) {
std::string date = values.next_string();
return date;
}
}
}
}
return "";
}

10
src/potential_file_reader.h
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@ -21,15 +21,17 @@
#include <string>
#include "pointers.h"
#include "text_file_reader.h"
namespace LAMMPS_NS
{
class PotentialFileReader : protected Pointers {
std::string potential_name;
TextFileReader * reader;
std::string filename;
static const int MAXLINE = 1024;
char line[MAXLINE];
FILE *fp;
std::string potential_name;
TextFileReader * open_potential(const std::string& path);
std::string get_potential_date(const std::string & path);
public:
PotentialFileReader(class LAMMPS *lmp, const std::string &filename, const std::string &potential_name);

117
src/text_file_reader.cpp Normal file
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@ -0,0 +1,117 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#include "lammps.h"
#include "force.h"
#include "error.h"
#include "comm.h"
#include "utils.h"
#include "text_file_reader.h"
#include "tokenizer.h"
#include "fmt/format.h"
#include <cstring>
using namespace LAMMPS_NS;
TextFileReader::TextFileReader(const std::string &filename, const std::string &filetype)
: filename(filename), filetype(filetype)
{
fp = fopen(filename.c_str(), "r");
if (fp == nullptr) {
throw FileReaderException(fmt::format("cannot open {} file {}", filetype, filename));
}
}
TextFileReader::~TextFileReader() {
fclose(fp);
}
void TextFileReader::skip_line() {
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
throw EOFException(fmt::format("Missing line in {} file!", filetype));
}
}
char *TextFileReader::next_line(int nparams) {
// concatenate lines until have nparams words
int n = 0;
int nwords = 0;
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
return nullptr;
}
// strip comment
if (ignore_comments && (ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords > 0) {
n = strlen(line);
}
while(nwords == 0 || nwords < nparams) {
char *ptr = fgets(&line[n], MAXLINE - n, fp);
if (ptr == nullptr) {
// EOF
if (nwords > 0 && nwords < nparams) {
throw EOFException(fmt::format("Incorrect format in {} file! {}/{} parameters", filetype.c_str(), nwords, nparams));
}
return nullptr;
}
// strip comment
if (ignore_comments && (ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
// skip line if blank
if (nwords > 0) {
n = strlen(line);
}
}
return line;
}
void TextFileReader::next_dvector(int n, double * list) {
int i = 0;
while (i < n) {
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
if (i < n) {
throw FileReaderException(fmt::format("Incorrect format in {} file! {}/{} values", filetype, i, n));
}
}
ValueTokenizer values(line);
while(values.has_next()) {
list[i++] = values.next_double();
}
}
}

68
src/text_file_reader.h Normal file
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@ -0,0 +1,68 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Richard Berger (Temple U)
------------------------------------------------------------------------- */
#ifndef LMP_TEXT_FILE_READER_H
#define LMP_TEXT_FILE_READER_H
#include <cstdio>
#include <string>
#include <exception>
namespace LAMMPS_NS
{
class TextFileReader {
std::string filename;
std::string filetype;
static const int MAXLINE = 1024;
char line[MAXLINE];
FILE *fp;
public:
bool ignore_comments;
TextFileReader(const std::string &filename, const std::string &filetype);
~TextFileReader();
void skip_line();
char * next_line(int nparams = 0);
void next_dvector(int n, double * list);
};
class FileReaderException : public std::exception {
std::string message;
public:
FileReaderException(const std::string & msg) : message(msg) {
}
~FileReaderException() throw() {
}
virtual const char * what() const throw() {
return message.c_str();
}
};
class EOFException : public FileReaderException {
public:
EOFException(const std::string & msg) : FileReaderException(msg) {
}
};
} // namespace LAMMPS_NS
#endif