import periodic table functions from VMD/molfile plugin
This commit is contained in:
Axel Kohlmeyer
@ -38,6 +38,22 @@
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#include <QWheelEvent>
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#include <QWidgetAction>
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#include <cmath>
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extern "C" {
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#include "periodic_table.h"
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static int get_pte_from_mass(double mass)
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{
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int idx = 0;
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for (int i = 0; i < nr_pte_entries; ++i)
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if (fabs(mass - pte_mass[i]) < 0.65) idx = i;
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if ((mass > 0.0) && (mass < 2.2)) idx = 1;
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// discriminate between Cobalt and Nickel. The loop will detect Nickel
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if ((mass < 61.24) && (mass > 58.8133)) idx = 27;
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return idx;
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}
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}
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static const QString blank(" ");
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ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidget *parent) :
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205
tools/lammps-gui/periodic_table.h
Executable file
205
tools/lammps-gui/periodic_table.h
Executable file
@ -0,0 +1,205 @@
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/***************************************************************************
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* RCS INFORMATION:
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*
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* $RCSfile: periodic_table.h,v $
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* $Author: johns $ $Locker: $ $State: Exp $
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* $Revision: 1.12 $ $Date: 2009/01/21 17:45:41 $
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*
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***************************************************************************/
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/*
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* periodic table of elements and helper functions to convert
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* ordinal numbers to labels and back.
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* all tables and functions are declared static, so that it
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* can be safely included by all plugins that may need it.
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*
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* 2002-2009 akohlmey@cmm.chem.upenn.edu, vmd@ks.uiuc.edu
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*/
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#include <string.h>
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#include <ctype.h>
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/* periodic table of elements for translation of ordinal to atom type */
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static const char *pte_label[] = {
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"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne",
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"Na", "Mg", "Al", "Si", "P" , "S", "Cl", "Ar", "K", "Ca", "Sc",
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"Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge",
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"As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc",
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"Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe",
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"Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb",
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"Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os",
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"Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr",
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"Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf",
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"Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt",
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"Ds", "Rg"
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};
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static const int nr_pte_entries = sizeof(pte_label) / sizeof(char *);
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/* corresponding table of masses. */
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static const double pte_mass[] = {
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/* X */ 0.00000, 1.00794, 4.00260, 6.941, 9.012182, 10.811,
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/* C */ 12.0107, 14.0067, 15.9994, 18.9984032, 20.1797,
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/* Na */ 22.989770, 24.3050, 26.981538, 28.0855, 30.973761,
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/* S */ 32.065, 35.453, 39.948, 39.0983, 40.078, 44.955910,
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/* Ti */ 47.867, 50.9415, 51.9961, 54.938049, 55.845, 58.9332,
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/* Ni */ 58.6934, 63.546, 65.409, 69.723, 72.64, 74.92160,
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/* Se */ 78.96, 79.904, 83.798, 85.4678, 87.62, 88.90585,
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/* Zr */ 91.224, 92.90638, 95.94, 98.0, 101.07, 102.90550,
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/* Pd */ 106.42, 107.8682, 112.411, 114.818, 118.710, 121.760,
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/* Te */ 127.60, 126.90447, 131.293, 132.90545, 137.327,
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/* La */ 138.9055, 140.116, 140.90765, 144.24, 145.0, 150.36,
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/* Eu */ 151.964, 157.25, 158.92534, 162.500, 164.93032,
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/* Er */ 167.259, 168.93421, 173.04, 174.967, 178.49, 180.9479,
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/* W */ 183.84, 186.207, 190.23, 192.217, 195.078, 196.96655,
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/* Hg */ 200.59, 204.3833, 207.2, 208.98038, 209.0, 210.0, 222.0,
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/* Fr */ 223.0, 226.0, 227.0, 232.0381, 231.03588, 238.02891,
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/* Np */ 237.0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0,
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/* Md */ 258.0, 259.0, 262.0, 261.0, 262.0, 266.0, 264.0, 269.0,
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/* Mt */ 268.0, 271.0, 272.0
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};
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/*
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* corresponding table of VDW radii.
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* van der Waals radii are taken from A. Bondi,
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* J. Phys. Chem., 68, 441 - 452, 1964,
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* except the value for H, which is taken from R.S. Rowland & R. Taylor,
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* J.Phys.Chem., 100, 7384 - 7391, 1996. Radii that are not available in
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* either of these publications have RvdW = 2.00 <20>.
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* The radii for Ions (Na, K, Cl, Ca, Mg, and Cs are based on the CHARMM27
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* Rmin/2 parameters for (SOD, POT, CLA, CAL, MG, CES) by default.
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*/
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static const double pte_vdw_radius[] = {
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/* X */ 1.5, 1.2, 1.4, 1.82, 2.0, 2.0,
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/* C */ 1.7, 1.55, 1.52, 1.47, 1.54,
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/* Na */ 1.36, 1.18, 2.0, 2.1, 1.8,
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/* S */ 1.8, 2.27, 1.88, 1.76, 1.37, 2.0,
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/* Ti */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
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/* Ni */ 1.63, 1.4, 1.39, 1.07, 2.0, 1.85,
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/* Se */ 1.9, 1.85, 2.02, 2.0, 2.0, 2.0,
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/* Zr */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
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/* Pd */ 1.63, 1.72, 1.58, 1.93, 2.17, 2.0,
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/* Te */ 2.06, 1.98, 2.16, 2.1, 2.0,
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/* La */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
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/* Eu */ 2.0, 2.0, 2.0, 2.0, 2.0,
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/* Er */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
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/* W */ 2.0, 2.0, 2.0, 2.0, 1.72, 1.66,
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/* Hg */ 1.55, 1.96, 2.02, 2.0, 2.0, 2.0, 2.0,
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/* Fr */ 2.0, 2.0, 2.0, 2.0, 2.0, 1.86,
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/* Np */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
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/* Md */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
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/* Mt */ 2.0, 2.0, 2.0
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};
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/* lookup functions */
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static const char *get_pte_label(const int idx)
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{
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if ((idx < 1) || (idx >= nr_pte_entries)) return pte_label[0];
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return pte_label[idx];
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}
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static double get_pte_mass(const int idx)
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{
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if ((idx < 1) || (idx >= nr_pte_entries)) return pte_mass[0];
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return pte_mass[idx];
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}
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static double get_pte_vdw_radius(const int idx)
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{
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if ((idx < 1) || (idx >= nr_pte_entries)) return pte_vdw_radius[0];
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#if 1
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/* Replace with Hydrogen radius with an "all-atom" radius */
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if (idx == 1)
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return 1.0; /* H */
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#else
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/* Replace with old VMD atom radii values */
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switch (idx) {
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case 1: return 1.0; /* H */
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case 6: return 1.5; /* C */
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case 7: return 1.4; /* N */
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case 8: return 1.3; /* O */
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case 9: return 1.2; /* F */
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case 15: return 1.5; /* P */
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case 16: return 1.9; /* S */
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}
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#endif
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return pte_vdw_radius[idx];
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}
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static int get_pte_idx(const char *label)
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{
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int i;
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char atom[3];
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/* zap string */
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atom[0] = (char) 0;
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atom[1] = (char) 0;
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atom[2] = (char) 0;
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/* if we don't have a null-pointer, there must be at least two
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* chars, which is all we need. we convert to the capitalization
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* convention of the table above during assignment. */
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if (label != NULL) {
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atom[0] = (char) toupper((int) label[0]);
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atom[1] = (char) tolower((int) label[1]);
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}
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/* discard numbers in atom label */
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if (isdigit(atom[1])) atom[1] = (char) 0;
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for (i=0; i < nr_pte_entries; ++i) {
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if ( (pte_label[i][0] == atom[0])
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&& (pte_label[i][1] == atom[1]) ) return i;
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}
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return 0;
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}
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static int get_pte_idx_from_string(const char *label) {
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int i, ind;
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char atom[3];
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if (label != NULL) {
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/* zap string */
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atom[0] = atom[1] = atom[2] = '\0';
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for (ind=0,i=0; (ind<2) && (label[i]!='\0'); i++) {
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if (label[i] != ' ') {
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atom[ind] = toupper(label[i]);
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ind++;
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}
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}
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if (ind < 1)
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return 0; /* no non-whitespace characters */
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for (i=0; i < nr_pte_entries; ++i) {
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if ((toupper(pte_label[i][0]) == atom[0]) && (toupper(pte_label[i][1]) == atom[1]))
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return i;
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}
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}
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return 0;
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}
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#if 0
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#include <stdio.h>
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int main() {
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int i;
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printf("Periodic table check/dump\n");
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printf(" Table contains data for %d elements\n", nr_pte_entries);
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printf(" Mass table size check: %d\n", sizeof(pte_mass) / sizeof(double));
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printf(" VDW table size check: %d\n", sizeof(pte_vdw_radius) / sizeof(double));
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printf("\n");
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printf("Symbol Num Mass rVDW\n");
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for (i=0; i<nr_pte_entries; i++) {
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printf(" %-2s %3d %6.2f %4.2f\n",
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get_pte_label(i), i, get_pte_mass(i), get_pte_vdw_radius(i));
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}
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return 0;
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}
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#endif
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