// Bob Hanson hansonr@stolaf.edu
// getPlaneGroups.spt
//
// 2024.09.28 Bob Hanson hansonr@stolaf.edu
//
// Create JSON of International Tables plane groups
//
// For generators and Wyckoff positions, we use trgen
// with flags what=gen and what=wpos. &trmat=c,-a-c,b is used rather than &trm=-y,-z,x-y
//
// for example:
//
// https://www.cryst.ehu.es/cgi-bin/plane/programs/nph-plane_getgen?gnum=5&what=gp&type=plane
// https://www.cryst.ehu.es/cgi-bin/plane/programs/nph-plane_getgen?gnum=5&what=gen&type=plane
//
// Output files are available in the src/org/jmol/symmetry/sg/json folder
//
// a bit of hardwiring:
targetDir = "c:/temp/bilbao/ita/";
// variables for the createJSONFiles call (below), after the functions
issues = [];
usetext = false;
itadelay = 0.1;
itaFirst = 0;
itaLast = 17;
itaForceNew = false;
ncleg = 0;
// only one function to run here:
function createJSONFiles(n, forceNew) {
// creates ita_.json, by space group
// n option to start at a given number (-30), or only a certain number (30), or all (0)
// forceNew option true to overwrite local files; false to use them if they are there.
var allSettings = [];
var allMore = [];
var allTransforms = [["i", "subtype", "clegId","det","hm","more"]]; // , "xyz"]];
//var allOps = [];
for (var i = 1; i <= itaLast; i++) {
if (n < 0 && i < -n || n > 0 && i != n) {
continue;
}
//_getAllOps(i, allOps);
var adata = _createJSONArray(i, forceNew, allSettings, allMore, allTransforms);
var thedata = adata.format("JSON");
var fname = targetDir + "jsonp/plane_" +i + ".json";
write var thedata @fname;
}
if (n == 0 || n == -1) {
allSettings += allMore;
var thedata = allSettings.format("JSON");
var fname = targetDir + "json/ita_all_plane.json";
write var thedata @fname;
for (var g in allSettings) {
if (g.gen) {
g.ngen = g.pop("gen").length;
g.ngp = g.pop("gp").length;
g.nwpos = g.pop("wpos").pos.length;
}
}
// fname = targetDir + "json/plane_list.json";
// thedata = allSettings.format("JSON");
// write var thedata @fname;
var thedata = allTransforms.join("\t",TRUE);
var fname = targetDir + "txt/cleg_settings_plane.tab";
write var thedata @fname;
print "done -- " + allSettings.length + " settings";
}
print issues;
}
function _getAllOps(sg, allOps) {
// "gp_full" does something different - ignored, and gets just generators
var y = _getITADataHTM(sg, 1, "gp", "", "", forceNew).split('| ")[2].split("")[1].trim().replace("\n"," |");
var ita = _fixName((y[i+1])[2][0].split("","_"));
allOps.push({"sg":i,"xyz":xyz,"ita":ita,"seitz":seitz,"m":m});
}
}
// all other functions are "private" to this script
function _createJSONArray(i, forceNew, allSettings, allMore, allTransforms) {
// Create ITA records for a specific space group.
// start by getting the ITA settings using getgen
// some reordering is done for groups 48, 50, 59, 68, and 78,
// which for some reason are not presented with the default (a,b,c) transformation
// as the first setting on the list.
var x = _getITADataHTM(i, 0, "", "", "", forceNew);
// this will be generators
var myTransforms = "";
//var x = x.split(" tag
// normalize -n/m to +(1-n/m); "+1," to ","
var gp = [];
var d = gdata.split("");
for (var j = 2; j <= d.length; j++) {
var xyz0 = d[j].split(" ")[2].split("<")[1];
var xyz = _fixUnitXYZ(xyz0 + "z");
gp.push(xyz);
}
return gp;
}
function _fixURI(s) {
return s.replace(" ","%20");
}
function _fixUnitXYZ(xyz) {
// this only for translation
// ITA gives non-normalized transformed operations for several settings, particularly when
// rotating to F from I or C from P in tetragonals, h to r in trigonals, and I to F in cubics.
// normalizes the code and removes the duplicated operators in case those are created
return (xyz + ",").replace("-1/2","+1/2").replace("-3/2","+1/2").replace("+3/2","+1/2").replace("-1/4","+3/4").replace("-3/4","+1/4").replace("-1/3","+2/3").replace("-2/3","+1/3").replace("-1/6","+5/6").replace("-5/6","+1/6").replace("-1/8","+7/8").replace("-3/8","+5/8").replace("-7/8","+1/8").replace("-1/12","+11/12").replace("-5/12","+7/12").replace("-7/12","+5/12").replace("-11/12","+1/12").replace("+1,",",")[1][-1];
}
function _getGeneratorJson(gdata, genOrgp) {
// parse the generator list using tags. All cases return two columns here,
// so we always just skip the first column.
var gen = [];
var y = gdata.split("");
if (y.length == 1) {
y= gdata.split(" ");
for (var j = 2; j <= y.length; j+=2) {
var coor = y[j].replace(" ","") + ",z";
gen.push(_fixUnitXYZ(coor));
}
} else {
for (var j = 5; j <= y.length; j += 3) {
var coor = y[j++].split("")[1] + "," + y[j++].split("")[1] + "," + y[j++].split("")[1];
gen.push(_fixUnitXYZ(coor));
}
}
return gen;
}
function _getWyckoffJson(its, gdata) {
// Wyckoff positions are a bit trickier.
// currently adding some Jmol-derived geometric elements here, just for the first member of the list.
var wyck = {};
var isUnconv = gdata.find("Standard/Default setting");
var w = gdata.split("Wyck");
var y = w[4].split('align="center">');
var pos = [];
wyck.pos = pos;
var n = 0;
var nctr = 0;
for (var j = 1; j <= y.length; j++) {
if (j == 1 && y[j].find("(")) {
var cent = [];
var c = y[j].split("th>")[0].split("+");
for (var k = 1; k <= c.length; k++) {
var cp = c[k].split("(")[2].split(")")[1].replace(" ","");
if (cp && cp != "0,0") {
cent.push(cp + ",0");
nctr++;
}
}
if (nctr > 0)
wyck.cent = cent;
continue;
}
if (j == 1)
continue;
var d = {};
d.mult = 0+y[j++].split("");
if (td.length == 1) {
td = "" + td.replace(")(",")(");
td = td.split("");
}
var coor = [];
for (var k = 1; k <= td.length; k++) {
var t = td[k];
if (t.find(')')) {
var p = t.split("(")[2].split(")")[1].replace(" ","");
coor.push(p + ",0");
}
}
d.mult = coor.length * (nctr + 1);
if (++n == 1) {
// skip first, which is general positions in a transformed format
d.geom = "general";
} else {
d.coord = coor;
d.geom = _getWyckoffElement(coor[1]);
}
pos.push(d);
}
return wyck;
}
function _getWyckoffElement(p) {
var xyz = p.split(",");
var n = 0;
var nxyz = ({});
for (var i = 1; i <= 3; i++) {
if (xyz[i].find('x')) {
nxyz |= 1;
}
if (xyz[i].find('y')) {
nxyz |= 2;
}
if (xyz[i].find('z')) {
nxyz |= 3;
}
}
switch (nxyz.length) {
case 0:
return "point";
case 1:
return "line";
case 2:
return "plane";
}
return "general";
}
// utility methods
function _fixName(s) {
// remove HTML markings, fix "unconv" :R
return (s.trim()
.replace("","").replace("","")
.replace("","").replace("","")
.replace("","").replace("","")
.replace("|","|")).replace(" "," ").replace(":R",":r");
}
m40 = [[0 0 0 0][0 0 0 0][0 0 0 0][0 0 0 1]];
function _toTransform(xyz){
// 1 0 -1 | 0
// 0 1 0 | 0
// 0 0 2 | 1/2
//
// x-z,y,2z+1/2 to "a,b,-a+2c;0,0,1/2 (transposed)
// a,b,-a+2c+1/2 also to "a,b,-a+2c;0,0,1/2 (not transposed)
// the function unitcell() runs org.jmol.symmetry.UnitCell.getMatrixAndUnitCell()
// unitcell() removes any embedded translations and puts the rotation in xyz-row,abc column format
// we get any embedded translation using symop()
var m = -unitcell(xyz, true);
var abc = symop(m, "xyz").replace('x','a').replace('y','b').replace('z','c');
var t = symop(xyz, "matrix")%2;
if (t == 0) {
return abc;
}
return abc + ";" + symop(m40 + t, "xyz");
}
function _toXYZ(abc){
// getGen needs the transposed matrix, in xyz format.
// this does the trick, as -m4 is the transpose of m4, and symop(matrix, "xyz")
// will accept a,b,c and return x,y,z
// check for translation and don't transpose that
var a = symop(abc, "matrix");
var t = a%2; // get translation vector
if (1.0 * t == 0) {
// transpose if no translation
a = -a;
} else {
// remove translation from 4x4, transpose it, then return translation
a = -(a + -t) + t;
}
return symop(a, "xyz");
}
function _getField(gdata, field, max) {
// get a &... field form a URL
var i = gdata.find(field + "=");
return (i == 0 ? "" : (gdata[i+field.length + 1][i+max] + "&").split("&")[1]);
}
createJSONFiles(itaFirst, itaForceNew);
/**
2024.09.28 new
|