SelectionCompiler.cpp

/*
 * Copyright (c) 2004-present, The University of Notre Dame. All rights
 * reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * 3. Neither the name of the copyright holder nor the names of its
 *    contributors may be used to endorse or promote products derived from
 *    this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#include "selection/SelectionCompiler.hpp"
 
#include <any>
#include <string>
 
#include "utils/StringUtils.hpp"
 
namespace OpenMD {
 
  bool SelectionCompiler::compile(const std::string& filename,
                                  const std::string& script) {
    this->filename = filename;
    this->script   = script;
    lineNumbers.clear();
    lineIndices.clear();
    aatokenCompiled.clear();
 
    if (internalCompile()) { return true; }
 
    std::size_t icharEnd;
    if ((icharEnd = script.find('\r', ichCurrentCommand)) ==
            std::string::npos &&
        (icharEnd = script.find('\n', ichCurrentCommand)) ==
            std::string::npos) {
      icharEnd = script.size();
    }
    errorLine = script.substr(ichCurrentCommand, icharEnd);
    return false;
  }
 
  bool SelectionCompiler::internalCompile() {
    cchScript   = script.size();
    ichToken    = 0;
    lineCurrent = 1;
 
    error = false;
 
    // std::vector<Token> lltoken;
    aatokenCompiled.clear();
    std::vector<Token> ltoken;
 
    Token tokenCommand;
    int tokCommand = Token::nada;
 
    for (; true; ichToken += cchToken) {
      if (lookingAtLeadingWhitespace()) continue;
      // if (lookingAtComment())
      //    continue;
      bool endOfLine = lookingAtEndOfLine();
      if (endOfLine || lookingAtEndOfStatement()) {
        if (tokCommand != Token::nada) {
          if (!compileCommand(ltoken)) { return false; }
          aatokenCompiled.push_back(atokenCommand);
          lineNumbers.push_back(lineCurrent);
          lineIndices.push_back(ichCurrentCommand);
          ltoken.clear();
          tokCommand = Token::nada;
        }
 
        if (ichToken < cchScript) {
          if (endOfLine) ++lineCurrent;
          continue;
        }
        break;
      }
 
      if (tokCommand != Token::nada) {
        if (lookingAtString()) {
          std::string str = getUnescapedStringLiteral();
          ltoken.push_back(Token(Token::string, str));
          continue;
        }
        // if ((tokCommand & Token::specialstring) != 0 &&
        //    lookingAtSpecialString()) {
        //    std::string str = script.substr(ichToken, ichToken + cchToken);
        //    ltoken.push_back(Token(Token::string, str));
        //    continue;
        //}
        // if (lookingAtDecimal((tokCommand & Token::negnums) != 0)) {
        if (lookingAtDecimal((tokCommand) != 0)) {
          float value = lexi_cast<float>(script.substr(ichToken, cchToken));
          ltoken.push_back(Token(Token::decimal, std::any(value)));
          continue;
        }
        // if (lookingAtInteger((tokCommand & Token::negnums) != 0)) {
        if (lookingAtInteger((tokCommand) != 0)) {
          int val = lexi_cast<int>(script.substr(ichToken, cchToken));
          ltoken.push_back(Token(Token::integer, std::any(val)));
          continue;
        }
      }
 
      if (lookingAtLookupToken()) {
        std::string ident = script.substr(ichToken, cchToken);
        Token token;
        Token* pToken = TokenMap::getInstance().getToken(ident);
        if (pToken != NULL) {
          token = *pToken;
        } else {
          token = Token(Token::identifier, ident);
        }
 
        int tok = token.tok;
 
        switch (tokCommand) {
        case Token::nada:
          ichCurrentCommand = ichToken;
          // tokenCommand = token;
          tokCommand = tok;
          if ((tokCommand & Token::command) == 0) return commandExpected();
          break;
 
        case Token::define:
          if (ltoken.size() == 1) {
            // we are looking at the variable name
            if (tok != Token::identifier &&
                (tok & Token::predefinedset) != Token::predefinedset)
              return invalidExpressionToken(ident);
          } else {
            // we are looking at the expression
            if (tok != Token::identifier &&
                (tok & (Token::expression | Token::predefinedset)) == 0)
              return invalidExpressionToken(ident);
          }
 
          break;
 
        case Token::select:
          if (tok != Token::identifier && (tok & Token::expression) == 0)
            return invalidExpressionToken(ident);
          break;
        }
        ltoken.push_back(token);
        continue;
      }
 
      if (ltoken.empty()) { return commandExpected(); }
 
      return unrecognizedToken();
    }
 
    return true;
  }
 
  bool SelectionCompiler::lookingAtLeadingWhitespace() {
    int ichT = ichToken;
    while (ichT < cchScript && std::isspace(script[ichT])) {
      ++ichT;
    }
    cchToken = ichT - ichToken;
    return cchToken > 0;
  }
 
  bool SelectionCompiler::lookingAtEndOfLine() {
    if (ichToken == cchScript) return true;
    int ichT = ichToken;
    char ch  = script[ichT];
    if (ch == '\r') {
      ++ichT;
      if (ichT < cchScript && script[ichT] == '\n') ++ichT;
    } else if (ch == '\n') {
      ++ichT;
    } else {
      return false;
    }
    cchToken = ichT - ichToken;
    return true;
  }
 
  bool SelectionCompiler::lookingAtEndOfStatement() {
    if (ichToken == cchScript || script[ichToken] != ';') return false;
    cchToken = 1;
    return true;
  }
 
  bool SelectionCompiler::lookingAtString() {
    if (ichToken == cchScript) return false;
    if (script[ichToken] != '"') return false;
    // remove support for single quote
    // in order to use it in atom expressions
    //    char chFirst = script.charAt(ichToken);
    //    if (chFirst != '"' && chFirst != '\'')
    //      return false;
    int ichT = ichToken + 1;
    //    while (ichT < cchScript && script.charAt(ichT++) != chFirst)
    char ch;
    bool previousCharBackslash = false;
    while (ichT < cchScript) {
      ch = script[ichT++];
      if (ch == '"' && !previousCharBackslash) break;
      previousCharBackslash = ch == '\\' ? !previousCharBackslash : false;
    }
    cchToken = ichT - ichToken;
 
    return true;
  }
 
  std::string SelectionCompiler::getUnescapedStringLiteral() {
    /** @todo */
    std::string sb(cchToken - 2, ' ');
 
    int ichMax = ichToken + cchToken - 1;
    int ich    = ichToken + 1;
 
    while (ich < ichMax) {
      char ch = script[ich++];
      if (ch == '\\' && ich < ichMax) {
        ch = script[ich++];
        switch (ch) {
        case 'b':
          ch = '\b';
          break;
        case 'n':
          ch = '\n';
          break;
        case 't':
          ch = '\t';
          break;
        case 'r':
          ch = '\r';
          // fall into
        case '"':
        case '\\':
        case '\'':
          break;
        case 'x':
        case 'u':
          int digitCount = ch == 'x' ? 2 : 4;
          if (ich < ichMax) {
            int unicode = 0;
            for (int k = digitCount; --k >= 0 && ich < ichMax;) {
              char chT  = script[ich];
              int hexit = getHexitValue(chT);
              if (hexit < 0) break;
              unicode <<= 4;
              unicode += hexit;
              ++ich;
            }
            ch = (char)unicode;
          }
        }
      }
      sb.append(1, ch);
    }
 
    return sb;
  }
 
  int SelectionCompiler::getHexitValue(char ch) {
    if (ch >= '0' && ch <= '9')
      return ch - '0';
    else if (ch >= 'a' && ch <= 'f')
      return 10 + ch - 'a';
    else if (ch >= 'A' && ch <= 'F')
      return 10 + ch - 'A';
    else
      return -1;
  }
 
  bool SelectionCompiler::lookingAtSpecialString() {
    int ichT = ichToken;
    char ch  = script[ichT];
    while (ichT < cchScript && ch != ';' && ch != '\r' && ch != '\n') {
      ++ichT;
    }
    cchToken = ichT - ichToken;
    return cchToken > 0;
  }
 
  bool SelectionCompiler::lookingAtDecimal(bool) {
    if (ichToken == cchScript) { return false; }
 
    int ichT = ichToken;
    if (script[ichT] == '-') { ++ichT; }
    bool digitSeen = false;
    char ch        = 'X';
    while (ichT < cchScript && std::isdigit(ch = script[ichT])) {
      ++ichT;
      digitSeen = true;
    }
 
    if (ichT == cchScript || ch != '.') { return false; }
 
    // to support DMPC.1, let's check the character before the dot
    if (ch == '.' && (ichT > 0) && std::isalpha(script[ichT - 1])) {
      return false;
    }
 
    ++ichT;
    while (ichT < cchScript && std::isdigit(script[ichT])) {
      ++ichT;
      digitSeen = true;
    }
    cchToken = ichT - ichToken;
    return digitSeen;
  }
 
  bool SelectionCompiler::lookingAtInteger(bool allowNegative) {
    if (ichToken == cchScript) { return false; }
    int ichT = ichToken;
    if (allowNegative && script[ichToken] == '-') { ++ichT; }
    int ichBeginDigits = ichT;
    while (ichT < cchScript && std::isdigit(script[ichT])) {
      ++ichT;
    }
    if (ichBeginDigits == ichT) { return false; }
    cchToken = ichT - ichToken;
    return isInteger(script.substr(ichToken, cchToken).c_str());
  }
 
  bool SelectionCompiler::lookingAtLookupToken() {
    if (ichToken == cchScript) { return false; }
 
    int ichT = ichToken;
    char ch;
    switch (ch = script[ichT++]) {
    case '(':
    case ')':
    case ',':
    case '[':
    case ']':
      break;
    case '&':
    case '|':
      if (ichT < cchScript && script[ichT] == ch) { ++ichT; }
      break;
    case '<':
    case '=':
    case '>':
      if (ichT < cchScript &&
          ((ch = script[ichT]) == '<' || ch == '=' || ch == '>')) {
        ++ichT;
      }
      break;
    case '/':
    case '!':
      if (ichT < cchScript && script[ichT] == '=') { ++ichT; }
      break;
    default:
      if ((ch < 'a' || ch > 'z') && (ch < 'A' && ch > 'Z') && ch != '_') {
        return false;
      }
      [[fallthrough]];
    case '*':
    case '?':  // include question marks in identifier for atom expressions
      while (ichT < cchScript && !std::isspace(ch = script[ichT]) &&
             (std::isalpha(ch) || std::isdigit(ch) || ch == '_' || ch == '.' ||
              ch == '*' || ch == '?' || ch == '+' || ch == '-' || ch == '[' ||
              ch == ']')) {
        ++ichT;
      }
      break;
    }
 
    cchToken = ichT - ichToken;
 
    return true;
  }
 
  bool SelectionCompiler::compileCommand(const std::vector<Token>& ltoken) {
    const Token& tokenCommand = ltoken[0];
    int tokCommand            = tokenCommand.tok;
 
    atokenCommand = ltoken;
    if ((tokCommand & Token::expressionCommand) != 0 && !compileExpression()) {
      return false;
    }
 
    return true;
  }
 
  bool SelectionCompiler::compileExpression() {
    /** todo */
    unsigned int i = 1;
    int tokCommand = atokenCommand[0].tok;
    if (tokCommand == Token::define) {
      i = 2;
    } else if ((tokCommand & Token::embeddedExpression) != 0) {
      // look for the open parenthesis
      while (i < atokenCommand.size() &&
             atokenCommand[i].tok != Token::leftparen)
        ++i;
    }
 
    if (i >= atokenCommand.size()) { return true; }
    return compileExpression(i);
  }
 
  bool SelectionCompiler::addTokenToPostfix(const Token& token) {
    ltokenPostfix.push_back(token);
    return true;
  }
 
  bool SelectionCompiler::compileExpression(int itoken) {
    ltokenPostfix.clear();
    for (int i = 0; i < itoken; ++i) {
      addTokenToPostfix(atokenCommand[i]);
    }
 
    atokenInfix = atokenCommand;
    itokenInfix = itoken;
 
    addTokenToPostfix(Token::tokenExpressionBegin);
    if (!clauseOr()) { return false; }
 
    addTokenToPostfix(Token::tokenExpressionEnd);
    if (itokenInfix != atokenInfix.size()) { return endOfExpressionExpected(); }
 
    atokenCommand = ltokenPostfix;
    return true;
  }
 
  Token SelectionCompiler::tokenNext() {
    if (itokenInfix == atokenInfix.size()) { return Token(); }
    return atokenInfix[itokenInfix++];
  }
 
  std::any SelectionCompiler::valuePeek() {
    if (itokenInfix == atokenInfix.size()) {
      return std::any();
    } else {
      return atokenInfix[itokenInfix].value;
    }
  }
 
  int SelectionCompiler::tokPeek() {
    if (itokenInfix == atokenInfix.size()) {
      return 0;
    } else {
      return atokenInfix[itokenInfix].tok;
    }
  }
 
  bool SelectionCompiler::clauseOr() {
    if (!clauseAnd()) { return false; }
 
    while (tokPeek() == Token::opOr) {
      Token tokenOr = tokenNext();
      if (!clauseAnd()) { return false; }
      addTokenToPostfix(tokenOr);
    }
    return true;
  }
 
  bool SelectionCompiler::clauseAnd() {
    if (!clauseNot()) { return false; }
 
    while (tokPeek() == Token::opAnd) {
      Token tokenAnd = tokenNext();
      if (!clauseNot()) { return false; }
      addTokenToPostfix(tokenAnd);
    }
    return true;
  }
 
  bool SelectionCompiler::clauseNot() {
    if (tokPeek() == Token::opNot) {
      Token tokenNot = tokenNext();
      if (!clauseNot()) { return false; }
      return addTokenToPostfix(tokenNot);
    }
    return clausePrimitive();
  }
 
  bool SelectionCompiler::clausePrimitive() {
    int tok = tokPeek();
    switch (tok) {
    case Token::within:
      return clauseWithin();
 
    case Token::alphahull:
      return clauseAlphaHull();
 
    case Token::asterisk:
    case Token::identifier:
      return clauseChemObjName();
 
    case Token::integer:
      return clauseIndex();
    default:
      if ((tok & Token::atomproperty) == Token::atomproperty) {
        return clauseComparator();
      }
      if ((tok & Token::predefinedset) != Token::predefinedset) { break; }
      // fall into the code and below and just add the token
      [[fallthrough]];
    case Token::all:
    case Token::none:
    case Token::hull:
      return addTokenToPostfix(tokenNext());
    case Token::leftparen:
      tokenNext();
      if (!clauseOr()) { return false; }
      if (tokenNext().tok != Token::rightparen) {
        return rightParenthesisExpected();
      }
      return true;
    }
    return unrecognizedExpressionToken();
  }
 
  bool SelectionCompiler::clauseComparator() {
    Token tokenAtomProperty = tokenNext();
    Token tokenComparator   = tokenNext();
    if ((tokenComparator.tok & Token::comparator) == 0) {
      return comparisonOperatorExpected();
    }
 
    Token tokenValue = tokenNext();
    if (tokenValue.tok != Token::integer && tokenValue.tok != Token::decimal) {
      return numberExpected();
    }
 
    float val;
    if (tokenValue.value.type() == typeid(int)) {
      val = std::any_cast<int>(tokenValue.value);
    } else if (tokenValue.value.type() == typeid(float)) {
      val = std::any_cast<float>(tokenValue.value);
    } else {
      return false;
    }
 
    std::any floatVal;
    floatVal = val;
    return addTokenToPostfix(
        Token(tokenComparator.tok, tokenAtomProperty.tok, floatVal));
  }
 
  bool SelectionCompiler::clauseWithin() {
    tokenNext();                                // WITHIN
    if (tokenNext().tok != Token::leftparen) {  // (
      return leftParenthesisExpected();
    }
 
    std::any distance;
    Token tokenDistance = tokenNext();  // distance
    switch (tokenDistance.tok) {
    case Token::integer:
    case Token::decimal:
      distance = tokenDistance.value;
      break;
    default:
      return numberOrKeywordExpected();
    }
 
    if (tokenNext().tok != Token::opOr) {  // ,
      return commaExpected();
    }
 
    if (!clauseOr()) {  // *expression*
      return false;
    }
 
    if (tokenNext().tok != Token::rightparen) {  // )T
      return rightParenthesisExpected();
    }
 
    return addTokenToPostfix(Token(Token::within, distance));
  }
 
  bool SelectionCompiler::clauseAlphaHull() {
    tokenNext();                                // alphaHull
    if (tokenNext().tok != Token::leftparen) {  // (
      return leftParenthesisExpected();
    }
 
    std::any alpha;
    Token tokenAlpha = tokenNext();  // alpha
    switch (tokenAlpha.tok) {
    case Token::integer:
    case Token::decimal:
      alpha = tokenAlpha.value;
      break;
    default:
      return numberOrKeywordExpected();
    }
 
    if (tokenNext().tok != Token::rightparen) {  // )T
      return rightParenthesisExpected();
    }
 
    return addTokenToPostfix(Token(Token::alphahull, alpha));
  }
 
  bool SelectionCompiler::clauseChemObjName() {
    Token token = tokenNext();
    if (token.tok == Token::identifier &&
        token.value.type() == typeid(std::string)) {
      std::string name = std::any_cast<std::string>(token.value);
      if (isNameValid(name)) {
        return addTokenToPostfix(Token(Token::name, name));
      } else {
        return compileError("invalid name: " + name);
      }
    }
 
    return false;
  }
 
  bool SelectionCompiler::isNameValid(const std::string& name) {
    int nbracket = 0;
    int ndot     = 0;
    for (unsigned int i = 0; i < name.size(); ++i) {
      switch (name[i]) {
      case '[':
        ++nbracket;
        break;
      case ']':
        --nbracket;
        break;
      case '.':
        ++ndot;
        break;
      }
    }
 
    // only allow 3 dots at most
    return (ndot <= 3 && nbracket == 0) ? true : false;
  }
 
  bool SelectionCompiler::clauseIndex() {
    Token token = tokenNext();
    if (token.tok == Token::integer) {
      int index = std::any_cast<int>(token.value);
      int tok   = tokPeek();
      if (tok == Token::to) {
        tokenNext();
        tok = tokPeek();
        if (tok != Token::integer) { return numberExpected(); }
 
        std::any intVal = tokenNext().value;
        int first       = index;
        if (intVal.type() != typeid(int)) { return false; }
        int second = std::any_cast<int>(intVal);
 
        return addTokenToPostfix(
            Token(Token::index, std::any(std::make_pair(first, second))));
 
      } else {
        return addTokenToPostfix(Token(Token::index, std::any(index)));
      }
    } else {
      return numberExpected();
    }
  }
}  // namespace OpenMD