atominfo.cc

大型并行量子化学软件；支持密度泛函（DFT）。可以进行各种量子化学计算。支持CHARMM并行计算。非常具有应用价值。

//
// molinfo.cc
//
// Copyright (C) 1996 Limit Point Systems, Inc.
//
// Author: Curtis Janssen <[e-mail]>
// Maintainer: LPS
//
// This file is part of the SC Toolkit.
//
// The SC Toolkit is free software; you can redistribute it and/or modify
// it under the terms of the GNU Library General Public License as published by
// the Free Software Foundation; either version 2, or (at your option)
// any later version.
//
// The SC Toolkit is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU Library General Public License for more details.
//
// You should have received a copy of the GNU Library General Public License
// along with the SC Toolkit; see the file COPYING.LIB.  If not, write to
// the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
//
// The U.S. Government is granted a limited license as per AL 91-7.
//

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <sys/stat.h>

#include <util/misc/units.h>
#include <util/misc/formio.h>
#include <util/state/stateio.h>
#include <util/group/message.h>
#include <chemistry/molecule/atominfo.h>

using namespace std;
using namespace sc;

////////////////////////////////////////////////////////////////////////
// AtomInfo

struct AtomInfo::atomname
AtomInfo::names_[MaxZ] = 
  {{"",           ""}, // 0
   {"hydrogen",   "H"}, // 1
   {"helium",     "He"}, // 2
   {"lithium",    "Li"}, // 3
   {"beryllium",  "Be"}, // 4
   {"boron",      "B"}, // 5
   {"carbon",     "C"}, // 6
   {"nitrogen",   "N"}, // 7
   {"oxygen",     "O"}, // 8
   {"fluorine",   "F"}, // 9
   {"neon",       "Ne"}, // 10
   {"sodium",     "Na"}, // 11
   {"magnesium",  "Mg"}, // 12
   {"aluminum",   "Al"}, // 13
   {"silicon",    "Si"}, // 14
   {"phosphorus" ,"P"}, // 15
   {"sulfur",     "S"}, // 16
   {"chlorine",   "Cl"}, // 17
   {"argon",      "Ar"}, // 18
   {"potassium",  "K"}, // 19
   {"calcium",    "Ca"}, // 20
   {"scandium",   "Sc"}, // 21
   {"titanium",   "Ti"}, // 22
   {"vanadium",   "V"}, // 23
   {"chromium",   "Cr"}, // 24
   {"manganese",  "Mn"}, // 25
   {"iron",       "Fe"}, // 26
   {"cobalt",     "Co"}, // 27
   {"nickel",     "Ni"}, // 28
   {"copper",     "Cu"}, // 29
   {"zinc",       "Zn"}, // 30
   {"gallium",    "Ga"}, // 31
   {"germanium",  "Ge"}, // 32
   {"arsenic",    "As"}, // 33
   {"selenium",   "Se"}, // 34
   {"bromine",    "Br"}, // 35
   {"krypton",    "Kr"}, // 36
   {"rubidium",     "Rb"}, // 37
   {"strontium",    "Sr"}, // 38
   {"yttrium",      "Y"}, // 39
   {"zirconium",    "Zr"}, // 40
   {"niobium",      "Nb"}, // 41
   {"molybdenum",   "Mo"}, // 42
   {"technetium",   "Tc"}, // 43
   {"ruthenium",    "Ru"}, // 44
   {"rhodium",      "Rh"}, // 45
   {"palladium",    "Pd"}, // 46
   {"silver",       "Ag"}, // 47
   {"cadminium",    "Cd"}, // 48
   {"indium",       "In"}, // 49
   {"tin",          "Sn"}, // 50
   {"antimony",     "Sb"}, // 51
   {"tellurium",    "Te"}, // 52
   {"iodine",       "I"}, // 53
   {"xenon",        "Xe"}, // 54
   {"cesium",       "Cs"}, // 55
   {"barium",       "Ba"}, // 56
   {"lanthanium",   "La"}, // 57
   {"cerium",       "Ce"}, // 58
   {"praseodymium", "Pr"}, // 59
   {"neodymium",    "Nd"}, // 60
   {"promethium",   "Pm"}, // 61
   {"samarium",     "Sm"}, // 62
   {"europium",     "Eu"}, // 63
   {"gadolinium",   "Gd"}, // 64
   {"terbium",      "Tb"}, // 65
   {"dysprosium",   "Dy"}, // 66
   {"holmium",      "Ho"}, // 67
   {"erbium",       "Er"}, // 68
   {"thulium",      "Tm"}, // 69
   {"ytterbium",    "Yb"}, // 70
   {"lutetium",     "Lu"}, // 71
   {"hafnium",      "Hf"}, // 72
   {"tantalum",     "Ta"}, // 73
   {"tungsten",     "W"}, // 74
   {"rhenium",      "Re"}, // 75
   {"osmium",       "Os"}, // 76
   {"iridium",      "Ir"}, // 77
   {"platinum",     "Pt"}, // 78
   {"gold",         "Au"}, // 79
   {"mercury",      "Hg"}, // 80
   {"thallium",     "Tl"}, // 81
   {"lead",         "Pb"}, // 82
   {"bismuth",      "Bi"}, // 83
   {"polonium",     "Po"}, // 84
   {"astatine",     "At"}, // 85
   {"radon",        "Rn"}, // 86
   {"francium",     "Fr"}, // 87
   {"radium",       "Ra"}, // 88
   {"actinium",     "Ac"}, // 89
   {"thorium",      "Th"}, // 90
   {"protactinium", "Pa"}, // 91
   {"uranium",      "U"}, // 92
   {"neptunium",    "Np"}, // 93
   {"plutonium",    "Pu"}, // 94
   {"americium",    "Am"}, // 95
   {"curium",       "Cm"}, // 96
   {"berkelium",    "Bk"}, // 97
   {"californium",  "Cf"}, // 98
   {"einsteinum",   "Es"}, // 99
   {"fermium",      "Fm"}, // 100
   {"mendelevium",  "Md"}, // 101
   {"nobelium",     "No"}, // 102
   {"lawrencium",   "Lr"}, // 103
   {"rutherfordium","Rf"}, // 104
   {"hahnium",      "Ha"}, // 105
   {"Unnamed",      "Un"}, // 106
   {"Unnamed",      "Un"} // 107
  };

static ClassDesc AtomInfo_cd(
  typeid(AtomInfo),"AtomInfo",3,"public SavableState",
  0, create<AtomInfo>, create<AtomInfo>);

AtomInfo::AtomInfo()
{
  overridden_values_ = 0;
  load_library_values();
}

AtomInfo::AtomInfo(const Ref<KeyVal>& keyval)
{
  overridden_values_ = 0;
  load_library_values();
  override_library_values(keyval);
}

AtomInfo::AtomInfo(StateIn& s):
  SavableState(s)
{
  if (s.node_to_node()) {
      s.get_array_double(mass_,MaxZ);
      s.get_array_double(atomic_radius_,MaxZ);
      s.get_array_double(vdw_radius_,MaxZ);
      s.get_array_double(bragg_radius_,MaxZ);
      s.get_array_double(maxprob_radius_,MaxZ);
      for (int i=0; i<MaxZ; i++) s.get_array_double(rgb_[i],3);
      s.getstring(overridden_values_);
      if (s.version(::class_desc<AtomInfo>()) >= 3) {
          s.get_array_double(ip_,MaxZ);
        }
    }
  else {
      overridden_values_ = 0;
      load_library_values();
      char *overrides;
      s.getstring(overrides);
      if (overrides) {
          Ref<ParsedKeyVal> keyval = new ParsedKeyVal;
          keyval->parse_string(overrides);
          override_library_values(keyval.pointer());
          delete[] overrides;
        }
    }
  if (s.version(::class_desc<AtomInfo>()) < 2) {
      atomic_radius_scale_ = 1.0;
      vdw_radius_scale_ = 1.0;
      bragg_radius_scale_ = 1.0;
      maxprob_radius_scale_ = 1.0;
    }
  else {
      s.get(atomic_radius_scale_);
      s.get(vdw_radius_scale_);
      s.get(bragg_radius_scale_);
      s.get(maxprob_radius_scale_);
    }
}

AtomInfo::~AtomInfo()
{
  delete[] overridden_values_;
}

void
AtomInfo::save_data_state(StateOut& s)
{
  if (s.node_to_node()) {
      s.put_array_double(mass_,MaxZ);
      s.put_array_double(atomic_radius_,MaxZ);
      s.put_array_double(vdw_radius_,MaxZ);
      s.put_array_double(bragg_radius_,MaxZ);
      s.put_array_double(maxprob_radius_,MaxZ);
      for (int i=0; i<MaxZ; i++) s.put_array_double(rgb_[i],3);
      s.put_array_double(ip_,MaxZ);
      s.putstring(overridden_values_);
    }
  else {
      s.putstring(overridden_values_);
    }
  s.put(atomic_radius_scale_);
  s.put(vdw_radius_scale_);
  s.put(bragg_radius_scale_);
  s.put(maxprob_radius_scale_);
}

void
AtomInfo::load_library_values()
{
  Ref<MessageGrp> grp = MessageGrp::get_default_messagegrp();
  if (grp->me() == 0) {
      const char* libdir;
      Ref<KeyVal> keyval;
      if ((libdir = getenv("SCLIBDIR")) != 0) {
          const char* atominfo = "/atominfo.kv";
          const char *eq = ::strchr(libdir,'=');
          if (eq) libdir = eq + 1;
          char *filename = new char[strlen(libdir) + strlen(atominfo) + 1];
          strcpy(filename, libdir);
          strcat(filename, atominfo);