Refactor SD update

[gromacs.git] / src / gromacs / fileio / readinp.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
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 * as published by the Free Software Foundation; either version 2.1
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#include "gmxpre.h"

#include "readinp.h"

#include <cstdlib>
#include <cstring>

#include <algorithm>

#include "gromacs/fileio/warninp.h"
#include "gromacs/utility/binaryinformation.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/niceheader.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/qsort_threadsafe.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textreader.h"
#include "gromacs/utility/textwriter.h"

t_inpfile *read_inpfile(gmx::TextInputStream *stream, const char *fn, int *ninp,
                        warninp_t wi)
{
    t_inpfile *inp = nullptr;

    if (debug)
    {
        fprintf(debug, "Reading MDP file %s\n", fn);
    }

    int             indexOfLineReadFromFile = 0;
    int             countOfUniqueKeysFound  = 0;
    std::string     line;
    gmx::TextReader reader(stream);
    reader.setTrimTrailingWhiteSpace(true);
    reader.setTrimTrailingComment(true, ';');
    while (reader.readLine(&line))
    {
        indexOfLineReadFromFile++;
        set_warning_line(wi, fn, indexOfLineReadFromFile);

        if (line.empty())
        {
            continue;
        }

        auto tokens = gmx::splitAndTrimDelimitedString(line, '=');
        if (tokens.size() < 2)
        {
            // TODO this seems like it silently ignores the user accidentally deleting an equals sign...
            if (debug)
            {
                fprintf(debug, "No = on line %d in file %s, ignored\n", indexOfLineReadFromFile, fn);
            }
            continue;
        }
        if (tokens.size() > 2)
        {
            // More than one equals symbol in the original line is
            // valid if the RHS is a free string, and needed for
            // "define = -DBOOLVAR -DVAR=VALUE".
            //
            // First, drop all the fields on the RHS of the first equals symbol.
            tokens.resize(1);
            // This find cannot return std::string::npos.
            auto firstEqualsPos = line.find('=');
            tokens.emplace_back(gmx::stripString(line.substr(firstEqualsPos + 1)));
        }
        if (tokens[0].empty())
        {
            // TODO ignoring such lines does not seem like good behaviour
            if (debug)
            {
                fprintf(debug, "Empty left hand side on line %d in file %s, ignored\n", indexOfLineReadFromFile, fn);
            }
            continue;
        }
        if (tokens[1].empty())
        {
            // TODO ignoring such lines does not seem like good behaviour
            if (debug)
            {
                fprintf(debug, "Empty right hand side on line %d in file %s, ignored\n", indexOfLineReadFromFile, fn);
            }
            continue;
        }

        /* Now finally something sensible; check for duplicates */
        int found_index = search_einp(countOfUniqueKeysFound, inp, tokens[0].c_str());

        if (found_index == -1)
        {
            /* add a new item */
            srenew(inp, ++countOfUniqueKeysFound);
            inp[countOfUniqueKeysFound-1].inp_count              = 1;
            inp[countOfUniqueKeysFound-1].count                  = 0;
            inp[countOfUniqueKeysFound-1].bObsolete              = FALSE;
            inp[countOfUniqueKeysFound-1].bHandledAsKeyValueTree = FALSE;
            inp[countOfUniqueKeysFound-1].bSet                   = FALSE;
            inp[countOfUniqueKeysFound-1].name                   = gmx_strdup(tokens[0].c_str());
            inp[countOfUniqueKeysFound-1].value                  = gmx_strdup(tokens[1].c_str());
        }
        else
        {
            auto message = gmx::formatString("Parameter \"%s\" doubly defined\n",
                                             tokens[0].c_str());
            warning_error(wi, message.c_str());
        }
    }
    /* This preserves the behaviour of the old code, which issues some
       warnings after completing parsing. Regenerating regressiontest
       warning files is not worth the effort. */
    indexOfLineReadFromFile++;
    set_warning_line(wi, fn, indexOfLineReadFromFile);

    if (debug)
    {
        fprintf(debug, "Done reading MDP file, there were %d entries in there\n",
                countOfUniqueKeysFound);
    }

    *ninp = countOfUniqueKeysFound;

    return inp;
}

gmx::KeyValueTreeObject flatKeyValueTreeFromInpFile(int ninp, t_inpfile inp[])
{
    gmx::KeyValueTreeBuilder  builder;
    auto                      root = builder.rootObject();
    for (int i = 0; i < ninp; ++i)
    {
        const char *value = inp[i].value;
        root.addValue<std::string>(inp[i].name, value != nullptr ? value : "");
    }
    return builder.build();
}


static int inp_comp(const void *a, const void *b)
{
    return (reinterpret_cast<const t_inpfile *>(a))->count - (reinterpret_cast<const t_inpfile *>(b))->count;
}

static void sort_inp(int ninp, t_inpfile inp[])
{
    int i, mm;

    mm = -1;
    for (i = 0; (i < ninp); i++)
    {
        mm = std::max(mm, inp[i].count);
    }
    for (i = 0; (i < ninp); i++)
    {
        if (inp[i].count == 0)
        {
            inp[i].count = mm++;
        }
    }
    gmx_qsort(inp, ninp, static_cast<size_t>(sizeof(inp[0])), inp_comp);
}

void write_inpfile(gmx::TextOutputStream *stream, const char *fn, int ninp, t_inpfile inp[],
                   gmx_bool bHaltOnUnknown,
                   WriteMdpHeader writeHeader,
                   warninp_t wi)
{
    using gmx::formatString;

    sort_inp(ninp, inp);

    gmx::TextWriter writer(stream);
    if (writeHeader == WriteMdpHeader::yes)
    {
        gmx::niceHeader(&writer, fn, ';');

        gmx::BinaryInformationSettings settings;
        settings.generatedByHeader(true);
        settings.linePrefix(";\t");
        gmx::printBinaryInformation(&writer, gmx::getProgramContext(), settings);
    }

    for (int i = 0; (i < ninp); i++)
    {
        if (inp[i].bHandledAsKeyValueTree)
        {
        }
        else if (inp[i].bSet)
        {
            if (inp[i].name[0] == ';' || (strlen(inp[i].name) > 2 && inp[i].name[1] == ';'))
            {
                writer.writeLine(formatString("%-24s", inp[i].name));
            }
            else
            {
                writer.writeLine(formatString("%-24s = %s", inp[i].name, inp[i].value ? inp[i].value : ""));
            }
        }
        else if (!inp[i].bObsolete)
        {
            auto message = formatString("Unknown left-hand '%s' in parameter file\n",
                                        inp[i].name);
            if (bHaltOnUnknown)
            {
                warning_error(wi, message.c_str());
            }
            else
            {
                warning(wi, message.c_str());
            }
        }
    }

    check_warning_error(wi, FARGS);
}

void replace_inp_entry(int ninp, t_inpfile *inp, const char *old_entry, const char *new_entry)
{
    int  i;

    for (i = 0; (i < ninp); i++)
    {
        if (gmx_strcasecmp_min(old_entry, inp[i].name) == 0)
        {
            if (new_entry)
            {
                fprintf(stderr, "Replacing old mdp entry '%s' by '%s'\n",
                        inp[i].name, new_entry);

                int foundIndex = search_einp(ninp, inp, new_entry);
                if (foundIndex >= 0)
                {
                    gmx_fatal(FARGS, "A parameter is present with both the old name '%s' and the new name '%s'.", inp[i].name, inp[foundIndex].name);
                }

                sfree(inp[i].name);
                inp[i].name = gmx_strdup(new_entry);
            }
            else
            {
                fprintf(stderr, "Ignoring obsolete mdp entry '%s'\n",
                        inp[i].name);
                inp[i].bObsolete = TRUE;
            }
        }
    }
}

int search_einp(int ninp, const t_inpfile *inp, const char *name)
{
    int i;

    if (inp == nullptr)
    {
        return -1;
    }
    for (i = 0; i < ninp; i++)
    {
        if (gmx_strcasecmp_min(name, inp[i].name) == 0)
        {
            return i;
        }
    }
    return -1;
}

void mark_einp_set(int ninp, t_inpfile *inp, const char *name)
{
    int i = search_einp(ninp, inp, name);
    if (i != -1)
    {
        inp[i].count = inp[0].inp_count++;
        inp[i].bSet  = TRUE;
        /* Prevent mdp lines being written twice for
           options that are handled via key-value trees. */
        inp[i].bHandledAsKeyValueTree = TRUE;

    }
}

static int get_einp(int *ninp, t_inpfile **inp, const char *name)
{
    int    i;
    int    notfound = FALSE;

    i = search_einp(*ninp, *inp, name);
    if (i == -1)
    {
        notfound = TRUE;
        i        = (*ninp)++;
        srenew(*inp, (*ninp));
        (*inp)[i].name                   = gmx_strdup(name);
        (*inp)[i].bSet                   = TRUE;
        (*inp)[i].bHandledAsKeyValueTree = FALSE;
        if (i == 0)
        {
            (*inp)[i].inp_count = 1;
        }
    }
    (*inp)[i].count = (*inp)[0].inp_count++;
    (*inp)[i].bSet  = TRUE;
    if (debug)
    {
        fprintf(debug, "Inp %d = %s\n", (*inp)[i].count, (*inp)[i].name);
    }

    /*if (i == (*ninp)-1)*/
    if (notfound)
    {
        return -1;
    }
    else
    {
        return i;
    }
}

/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
int get_eint(int *ninp, t_inpfile **inp, const char *name, int def,
             warninp_t wi)
{
    char buf[32], *ptr, warn_buf[STRLEN];
    int  ii;
    int  ret;

    ii = get_einp(ninp, inp, name);

    if (ii == -1)
    {
        sprintf(buf, "%d", def);
        (*inp)[(*ninp)-1].value = gmx_strdup(buf);

        return def;
    }
    else
    {
        ret = std::strtol((*inp)[ii].value, &ptr, 10);
        if (*ptr != '\0')
        {
            sprintf(warn_buf, "Right hand side '%s' for parameter '%s' in parameter file is not an integer value\n", (*inp)[ii].value, (*inp)[ii].name);
            warning_error(wi, warn_buf);
        }

        return ret;
    }
}

/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
gmx_int64_t get_eint64(int *ninp, t_inpfile **inp,
                       const char *name, gmx_int64_t def,
                       warninp_t wi)
{
    char            buf[32], *ptr, warn_buf[STRLEN];
    int             ii;
    gmx_int64_t     ret;

    ii = get_einp(ninp, inp, name);

    if (ii == -1)
    {
        sprintf(buf, "%" GMX_PRId64, def);
        (*inp)[(*ninp)-1].value = gmx_strdup(buf);

        return def;
    }
    else
    {
        ret = str_to_int64_t((*inp)[ii].value, &ptr);
        if (*ptr != '\0')
        {
            sprintf(warn_buf, "Right hand side '%s' for parameter '%s' in parameter file is not an integer value\n", (*inp)[ii].value, (*inp)[ii].name);
            warning_error(wi, warn_buf);
        }

        return ret;
    }
}

/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
double get_ereal(int *ninp, t_inpfile **inp, const char *name, double def,
                 warninp_t wi)
{
    char   buf[32], *ptr, warn_buf[STRLEN];
    int    ii;
    double ret;

    ii = get_einp(ninp, inp, name);

    if (ii == -1)
    {
        sprintf(buf, "%g", def);
        (*inp)[(*ninp)-1].value = gmx_strdup(buf);

        return def;
    }
    else
    {
        ret = strtod((*inp)[ii].value, &ptr);
        if (*ptr != '\0')
        {
            sprintf(warn_buf, "Right hand side '%s' for parameter '%s' in parameter file is not a real value\n", (*inp)[ii].value, (*inp)[ii].name);
            warning_error(wi, warn_buf);
        }

        return ret;
    }
}

/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
const char *get_estr(int *ninp, t_inpfile **inp, const char *name, const char *def)
{
    char buf[32];
    int  ii;

    ii = get_einp(ninp, inp, name);

    if (ii == -1)
    {
        if (def)
        {
            sprintf(buf, "%s", def);
            (*inp)[(*ninp)-1].value = gmx_strdup(buf);
        }
        else
        {
            (*inp)[(*ninp)-1].value = nullptr;
        }

        return def;
    }
    else
    {
        return (*inp)[ii].value;
    }
}

/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
int get_eeenum(int *ninp, t_inpfile **inp, const char *name, const char **defs,
               warninp_t wi)
{
    int  ii, i, j;
    int  n = 0;
    char buf[STRLEN];

    ii = get_einp(ninp, inp, name);

    if (ii == -1)
    {
        (*inp)[(*ninp)-1].value = gmx_strdup(defs[0]);

        return 0;
    }

    for (i = 0; (defs[i] != nullptr); i++)
    {
        if (gmx_strcasecmp_min(defs[i], (*inp)[ii].value) == 0)
        {
            break;
        }
    }

    if (defs[i] == nullptr)
    {
        n += sprintf(buf, "Invalid enum '%s' for variable %s, using '%s'\n",
                     (*inp)[ii].value, name, defs[0]);
        n += sprintf(buf+n, "Next time use one of:");
        j  = 0;
        while (defs[j])
        {
            n += sprintf(buf+n, " '%s'", defs[j]);
            j++;
        }
        if (wi != nullptr)
        {
            warning_error(wi, buf);
        }
        else
        {
            fprintf(stderr, "%s\n", buf);
        }

        (*inp)[ii].value = gmx_strdup(defs[0]);

        return 0;
    }

    return i;
}

int get_eenum(int *ninp, t_inpfile **inp, const char *name, const char **defs)
{
    return get_eeenum(ninp, inp, name, defs, nullptr);
}