#pragma once
#ifndef __enviromental_variables__
#include "env_var.h"
#include "MCECavity.h"
#include <vector>
#include <string>
#endif
#include "VoxelMap.h"
#define MAX_AT_PROPERTIES 255
#define _ATOM_VARIABLES_
#ifdef _VAR_ATOM_H_
using namespace std;
ElementDescription AtomProperties[MAX_AT_PROPERTIES];
int m_nElementsNumber;
//The atomic form factors were taken from the International Tables for Crystallography
//http://lamp.tu-graz.ac.at/~hadley/ss1/crystaldiffraction/atomicformfactors/formfactors.php
AtomicFormFactor AtFormFactors[211] = {
{"H",0.489918,20.6593,0.262003,7.74039,0.196767,49.5519,0.049879,2.20159,0.001305},
{"H1-",0.897661,53.1368,0.565616,15.187,0.415815,186.576,0.116973,3.56709,0.002389},
{"He",0.8734,9.1037,0.6309,3.3568,0.3112,22.9276,0.178,0.9821,0.0064},
{"Li",1.1282,3.9546,0.7508,1.0524,0.6175,85.3905,0.4653,168.261,0.0377},
{"Li1+",0.6968,4.6237,0.7888,1.9557,0.3414,0.6316,0.1563,10.0953,0.0167},
{"Be",1.5919,43.6427,1.1278,1.8623,0.5391,103.483,0.7029,0.542,0.0385},
{"Be2+",6.2603,0.0027,0.8849,0.8313,0.7993,2.2758,0.1647,5.1146,-6.1092},
{"B",2.0545,23.2185,1.3326,1.021,1.0979,60.3498,0.7068,0.1403,-0.1932},
{"C",2.31,20.8439,1.02,10.2075,1.5886,0.5687,0.865,51.6512,0.2156},
{"Cval",2.26069,22.6907,1.56165,0.656665,1.05075,9.75618,0.839259,55.5949,0.286977},
{"N",12.2126,0.0057,3.1322,9.8933,2.0125,28.9975,1.1663,0.5826,-11.529},
{"O",3.0485,13.2771,2.2868,5.7011,1.5463,0.3239,0.867,32.9089,0.2508},
{"O1-",4.1916,12.8573,1.63969,4.17236,1.52673,47.0179,-20.307,-0.01404,21.9412},
{"F",3.5392,10.2825,2.6412,4.2944,1.517,0.2615,1.0243,26.1476,0.2776},
{"F1-",3.6322,5.27756,3.51057,14.7353,1.26064,0.442258,0.940706,47.3437,0.653396},
{"Ne",3.9553,8.4042,3.1125,3.4262,1.4546,0.2306,1.1251,21.7184,0.3515},
{"Na",4.7626,3.285,3.1736,8.8422,1.2674,0.3136,1.1128,129.424,0.676},
{"Na1+",3.2565,2.6671,3.9362,6.1153,1.3998,0.2001,1.0032,14.039,0.404},
{"Mg",5.4204,2.8275,2.1735,79.2611,1.2269,0.3808,2.3073,7.1937,0.8584},
{"Mg2+",3.4988,2.1676,3.8378,4.7542,1.3284,0.185,0.8497,10.1411,0.4853},
{"Al",6.4202,3.0387,1.9002,0.7426,1.5936,31.5472,1.9646,85.0886,1.1151},
{"Al3+",4.17448,1.93816,3.3876,4.14553,1.20296,0.228753,0.528137,8.28524,0.706786},
{"Siv",6.2915,2.4386,3.0353,32.3337,1.9891,0.6785,1.541,81.6937,1.1407},
{"Sival",5.66269,2.6652,3.07164,38.6634,2.62446,0.916946,1.3932,93.5458,1.24707},
{"Si4+",4.43918,1.64167,3.20345,3.43757,1.19453,0.2149,0.41653,6.65365,0.746297},
{"P",6.4345,1.9067,4.1791,27.157,1.78,0.526,1.4908,68.1645,1.1149},
{"S",6.9053,1.4679,5.2034,22.2151,1.4379,0.2536,1.5863,56.172,0.8669},
{"Cl",11.4604,0.0104,7.1964,1.1662,6.2556,18.5194,1.6455,47.7784,-9.5574},
{"Cl1-",18.2915,0.0066,7.2084,1.1717,6.5337,19.5424,2.3386,60.4486,-16.378},
{"Ar",7.4845,0.9072,6.7723,14.8407,0.6539,43.8983,1.6442,33.3929,1.4445},
{"K",8.2186,12.7949,7.4398,0.7748,1.0519,213.187,0.8659,41.6841,1.4228},
{"K1+",7.9578,12.6331,7.4917,0.7674,6.359,-0.002,1.1915,31.9128,-4.9978},
{"Ca",8.6266,10.4421,7.3873,0.6599,1.5899,85.7484,1.0211,178.437,1.3751},
{"Ca2+",15.6348,-0.0074,7.9518,0.6089,8.4372,10.3116,0.8537,25.9905,-14.875},
{"Sc",9.189,9.0213,7.3679,0.5729,1.6409,136.108,1.468,51.3531,1.3329},
{"Sc3+",13.4008,0.29854,8.0273,7.9629,1.65943,-0.28604,1.57936,16.0662,-6.6667},
{"Ti",9.7595,7.8508,7.3558,0.5,1.6991,35.6338,1.9021,116.105,1.2807},
{"Ti2+",9.11423,7.5243,7.62174,0.457585,2.2793,19.5361,0.087899,61.6558,0.897155},
{"Ti3+",17.7344,0.22061,8.73816,7.04716,5.25691,-0.15762,1.92134,15.9768,-14.652},
{"Ti4+",19.5114,0.178847,8.23473,6.67018,2.01341,-0.29263,1.5208,12.9464,-13.28},
{"V",10.2971,6.8657,7.3511,0.4385,2.0703,26.8938,2.0571,102.478,1.2199},
{"V2+",10.106,6.8818,7.3541,0.4409,2.2884,20.3004,0.0223,115.122,1.2298},
{"V3+",9.43141,6.39535,7.7419,0.383349,2.15343,15.1908,0.016865,63.969,0.656565},
{"V5+",15.6887,0.679003,8.14208,5.40135,2.03081,9.97278,-9.576,0.940464,1.7143},
{"Cr",10.6406,6.1038,7.3537,0.392,3.324,20.2626,1.4922,98.7399,1.1832},
{"Cr2+",9.54034,5.66078,7.7509,0.344261,3.58274,13.3075,0.509107,32.4224,0.616898},
{"Cr3+",9.6809,5.59463,7.81136,0.334393,2.87603,12.8288,0.113575,32.8761,0.518275},
{"Mn",11.2819,5.3409,7.3573,0.3432,3.0193,17.8674,2.2441,83.7543,1.0896},
{"Mn2+",10.8061,5.2796,7.362,0.3435,3.5268,14.343,0.2184,41.3235,1.0874},
{"Mn3+",9.84521,4.91797,7.87194,0.294393,3.56531,10.8171,0.323613,24.1281,0.393974},
{"Mn4+",9.96253,4.8485,7.97057,0.283303,2.76067,10.4852,0.054447,27.573,0.251877},
{"Fe",11.7695,4.7611,7.3573,0.3072,3.5222,15.3535,2.3045,76.8805,1.0369},
{"Fe2+",11.0424,4.6538,7.374,0.3053,4.1346,12.0546,0.4399,31.2809,1.0097},
{"Fe3+",11.1764,4.6147,7.3863,0.3005,3.3948,11.6729,0.0724,38.5566,0.9707},
{"Co",12.2841,4.2791,7.3409,0.2784,4.0034,13.5359,2.3488,71.1692,1.0118},
{"Co2+",11.2296,4.1231,7.3883,0.2726,4.7393,10.2443,0.7108,25.6466,0.9324},
{"Co3+",10.338,3.90969,7.88173,0.238668,4.76795,8.35583,0.725591,18.3491,0.286667},
{"Ni",12.8376,3.8785,7.292,0.2565,4.4438,12.1763,2.38,66.3421,1.0341},
{"Ni2+",11.4166,3.6766,7.4005,0.2449,5.3442,8.873,0.9773,22.1626,0.8614},
{"Ni3+",10.7806,3.5477,7.75868,0.22314,5.22746,7.64468,0.847114,16.9673,0.386044},
{"Cu",13.338,3.5828,7.1676,0.247,5.6158,11.3966,1.6735,64.8126,1.191},
{"Cu1+",11.9475,3.3669,7.3573,0.2274,6.2455,8.6625,1.5578,25.8487,0.89},
{"Cu2+",11.8168,3.37484,7.11181,0.244078,5.78135,7.9876,1.14523,19.897,1.14431},
{"Zn",14.0743,3.2655,7.0318,0.2333,5.1652,10.3163,2.41,58.7097,1.3041},
{"Zn2+",11.9719,2.9946,7.3862,0.2031,6.4668,7.0826,1.394,18.0995,0.7807},
{"Ga",15.2354,3.0669,6.7006,0.2412,4.3591,10.7805,2.9623,61.4135,1.7189},
{"Ga3+",12.692,2.81262,6.69883,0.22789,6.06692,6.36441,1.0066,14.4122,1.53545},
{"Ge",16.0816,2.8509,6.3747,0.2516,3.7068,11.4468,3.683,54.7625,2.1313},
{"Ge4+",12.9172,2.53718,6.70003,0.205855,6.06791,5.47913,0.859041,11.603,1.45572},
{"As",16.6723,2.6345,6.0701,0.2647,3.4313,12.9479,4.2779,47.7972,2.531},
{"Se",17.0006,2.4098,5.8196,0.2726,3.9731,15.2372,4.3543,43.8163,2.8409},
{"Br",17.1789,2.1723,5.2358,16.5796,5.6377,0.2609,3.9851,41.4328,2.9557},
{"Br1-",17.1718,2.2059,6.3338,19.3345,5.5754,0.2871,3.7272,58.1535,3.1776},
{"Kr",17.3555,1.9384,6.7286,16.5623,5.5493,0.2261,3.5375,39.3972,2.825},
{"Rb",17.1784,1.7888,9.6435,17.3151,5.1399,0.2748,1.5292,164.934,3.4873},
{"Rb1+",17.5816,1.7139,7.6598,14.7957,5.8981,0.1603,2.7817,31.2087,2.0782},
{"Sr",17.5663,1.5564,9.8184,14.0988,5.422,0.1664,2.6694,132.376,2.5064},
{"Sr2+",18.0874,1.4907,8.1373,12.6963,2.5654,24.5651,-34.193,-0.0138,41.4025},
{"Y",17.776,1.4029,10.2946,12.8006,5.72629,0.125599,3.26588,104.354,1.91213},
{"Y3+",17.9268,1.35417,9.1531,11.2145,1.76795,22.6599,-33.108,-0.01319,40.2602},
{"Zr",17.8765,1.27618,10.948,11.916,5.41732,0.117622,3.65721,87.6627,2.06929},
{"Zr4+",18.1668,1.2148,10.0562,10.1483,1.01118,21.6054,-2.6479,-0.10276,9.41454},
{"Nb",17.6142,1.18865,12.0144,11.766,4.04183,0.204785,3.53346,69.7957,3.75591},
{"Nb3+",19.8812,0.019175,18.0653,1.13305,11.0177,10.1621,1.94715,28.3389,-12.912},
{"Nb5+",17.9163,1.12446,13.3417,0.028781,10.799,9.28206,0.337905,25.7228,-6.3934},
{"Mo",3.7025,0.2772,17.2356,1.0958,12.8876,11.004,3.7429,61.6584,4.3875},
{"Mo3+",21.1664,0.014734,18.2017,1.03031,11.7423,9.53659,2.30951,26.6307,-14.421},
{"Mo5+",21.0149,0.014345,18.0992,1.02238,11.4632,8.78809,0.740625,23.3452,-14.316},
{"Mo6+",17.8871,1.03649,11.175,8.48061,6.57891,0.058881,0,0,0.344941},
{"Tc",19.1301,0.864132,11.0948,8.14487,4.64901,21.5707,2.71263,86.8472,5.40428},
{"Ru",19.2674,0.80852,12.9182,8.43467,4.86337,24.7997,1.56756,94.2928,5.37874},
{"Ru3+",18.5638,0.847329,13.2885,8.37164,9.32602,0.017662,3.00964,22.887,-3.1892},
{"Ru4+",18.5003,0.844582,13.1787,8.12534,4.71304,0.36495,2.18535,20.8504,1.42357},
{"Rh",19.2957,0.751536,14.3501,8.21758,4.73425,25.8749,1.28918,98.6062,5.328},
{"Rh3+",18.8785,0.764252,14.1259,7.84438,3.32515,21.2487,-6.1989,-0.01036,11.8678},
{"Rh4+",18.8545,0.760825,13.9806,7.62436,2.53464,19.3317,-5.6526,-0.0102,11.2835},
{"Pd",19.3319,0.698655,15.5017,7.98929,5.29537,25.2052,0.605844,76.8986,5.26593},
{"Pd2+",19.1701,0.696219,15.2096,7.55573,4.32234,22.5057,0,0,5.2916},
{"Pd4+",19.2493,0.683839,14.79,7.14833,2.89289,17.9144,-7.9492,0.005127,13.0174},
{"Ag",19.2808,0.6446,16.6885,7.4726,4.8045,24.6605,1.0463,99.8156,5.179},
{"Ag1+",19.1812,0.646179,15.9719,7.19123,5.27475,21.7326,0.357534,66.1147,5.21572},
{"Ag2+",19.1643,0.645643,16.2456,7.18544,4.3709,21.4072,0,0,5.21404},
{"Cd",19.2214,0.5946,17.6444,6.9089,4.461,24.7008,1.6029,87.4825,5.0694},
{"Cd2+",19.1514,0.597922,17.2535,6.80639,4.47128,20.2521,0,0,5.11937},
{"In",19.1624,0.5476,18.5596,6.3776,4.2948,25.8499,2.0396,92.8029,4.9391},
{"In3+",19.1045,0.551522,18.1108,6.3247,3.78897,17.3595,0,0,4.99635},
{"Sn",19.1889,5.8303,19.1005,0.5031,4.4585,26.8909,2.4663,83.9571,4.7821},
{"Sn2+",19.1094,0.5036,19.0548,5.8378,4.5648,23.3752,0.487,62.2061,4.7861},
{"Sn4+",18.9333,5.764,19.7131,0.4655,3.4182,14.0049,0.0193,-0.7583,3.9182},
{"Sb",19.6418,5.3034,19.0455,0.4607,5.0371,27.9074,2.6827,75.2825,4.5909},
{"Sb3+",18.9755,0.467196,18.933,5.22126,5.10789,19.5902,0.288753,55.5113,4.69626},
{"Sb5+",19.8685,5.44853,19.0302,0.467973,2.41253,14.1259,0,0,4.69263},
{"Te",19.9644,4.81742,19.0138,0.420885,6.14487,28.5284,2.5239,70.8403,4.352},
{"I",20.1472,4.347,18.9949,0.3814,7.5138,27.766,2.2735,66.8776,4.0712},
{"I1-",20.2332,4.3579,18.997,0.3815,7.8069,29.5259,2.8868,84.9304,4.0714},
{"Xe",20.2933,3.9282,19.0298,0.344,8.9767,26.4659,1.99,64.2658,3.7118},
{"Cs",20.3892,3.569,19.1062,0.3107,10.662,24.3879,1.4953,213.904,3.3352},
{"Cs1+",20.3524,3.552,19.1278,0.3086,10.2821,23.7128,0.9615,59.4565,3.2791},
{"Ba",20.3361,3.216,19.297,0.2756,10.888,20.2073,2.6959,167.202,2.7731},
{"Ba2+",20.1807,3.21367,19.1136,0.28331,10.9054,20.0558,0.77634,51.746,3.02902},
{"La",20.578,2.94817,19.599,0.244475,11.3727,18.7726,3.28719,133.124,2.14678},
{"La3+",20.2489,2.9207,19.3763,0.250698,11.6323,17.8211,0.336048,54.9453,2.4086},
{"Ce",21.1671,2.81219,19.7695,0.226836,11.8513,17.6083,3.33049,127.113,1.86264},
{"Ce3+",20.8036,2.77691,19.559,0.23154,11.9369,16.5408,0.612376,43.1692,2.09013},
{"Ce4+",20.3235,2.65941,19.8186,0.21885,12.1233,15.7992,0.144583,62.2355,1.5918},
{"Pr",22.044,2.77393,19.6697,0.222087,12.3856,16.7669,2.82428,143.644,2.0583},
{"Pr3+",21.3727,2.6452,19.7491,0.214299,12.1329,15.323,0.97518,36.4065,1.77132},
{"Pr4+",20.9413,2.54467,20.0539,0.202481,12.4668,14.8137,0.296689,45.4643,1.24285},
{"Nd",22.6845,2.66248,19.6847,0.210628,12.774,15.885,2.85137,137.903,1.98486},
{"Nd3+",21.961,2.52722,19.9339,0.199237,12.12,14.1783,1.51031,30.8717,1.47588},
{"Pm",23.3405,2.5627,19.6095,0.202088,13.1235,15.1009,2.87516,132.721,2.02876},
{"Pm3+",22.5527,2.4174,20.1108,0.185769,12.0671,13.1275,2.07492,27.4491,1.19499},
{"Sm",24.0042,2.47274,19.4258,0.196451,13.4396,14.3996,2.89604,128.007,2.20963},
{"Sm3+",23.1504,2.31641,20.2599,0.174081,11.9202,12.1571,2.71488,24.8242,0.954586},
{"Eu",24.6274,2.3879,19.0886,0.1942,13.7603,13.7546,2.9227,123.174,2.5745},
{"Eu2+",24.0063,2.27783,19.9504,0.17353,11.8034,11.6096,3.87243,26.5156,1.36389},
{"Eu3+",23.7497,2.22258,20.3745,0.16394,11.8509,11.311,3.26503,22.9966,0.759344},
{"Gd",25.0709,2.25341,19.0798,0.181951,13.8518,12.9331,3.54545,101.398,2.4196},
{"Gd3+",24.3466,2.13553,20.4208,0.155525,11.8708,10.5782,3.7149,21.7029,0.645089},
{"Tb",25.8976,2.24256,18.2185,0.196143,14.3167,12.6648,2.95354,115.362,3.58324},
{"Tb3+",24.9559,2.05601,20.3271,0.149525,12.2471,10.0499,3.773,21.2773,0.691967},
{"Dy",26.507,2.1802,17.6383,0.202172,14.5596,12.1899,2.96577,111.874,4.29728},
{"Dy3+",25.5395,1.9804,20.2861,0.143384,11.9812,9.34972,4.50073,19.581,0.68969},
{"Ho",26.9049,2.07051,17.294,0.19794,14.5583,11.4407,3.63837,92.6566,4.56796},
{"Ho3+",26.1296,1.91072,20.0994,0.139358,11.9788,8.80018,4.93676,18.5908,0.852795},
{"Er",27.6563,2.07356,16.4285,0.223545,14.9779,11.3604,2.98233,105.703,5.92046},
{"Er3+",26.722,1.84659,19.7748,0.13729,12.1506,8.36225,5.17379,17.8974,1.17613},
{"Tm",28.1819,2.02859,15.8851,0.238849,15.1542,10.9975,2.98706,102.961,6.75621},
{"Tm3+",27.3083,1.78711,19.332,0.136974,12.3339,7.96778,5.38348,17.2922,1.63929},
{"Yb",28.6641,1.9889,15.4345,0.257119,15.3087,10.6647,2.98963,100.417,7.56672},
{"Yb2+",28.1209,1.78503,17.6817,0.15997,13.3335,8.18304,5.14657,20.39,3.70983},
{"Yb3+",27.8917,1.73272,18.7614,0.13879,12.6072,7.64412,5.47647,16.8153,2.26001},
{"Lu",28.9476,1.90182,15.2208,9.98519,15.1,0.261033,3.71601,84.3298,7.97628},
{"Lu3+",28.4628,1.68216,18.121,0.142292,12.8429,7.33727,5.59415,16.3535,2.97573},
{"Hf",29.144,1.83262,15.1726,9.5999,14.7586,0.275116,4.30013,72.029,8.58154},
{"Hf4+",28.8131,1.59136,18.4601,0.128903,12.7285,6.76232,5.59927,14.0366,2.39699},
{"Ta",29.2024,1.77333,15.2293,9.37046,14.5135,0.295977,4.76492,63.3644,9.24354},
{"Ta5+",29.1587,1.50711,18.8407,0.116741,12.8268,6.31524,5.38695,12.4244,1.78555},
{"W",29.0818,1.72029,15.43,9.2259,14.4327,0.321703,5.11982,57.056,9.8875},
{"W6+",29.4936,1.42755,19.3763,0.104621,13.0544,5.93667,5.06412,11.1972,1.01074},
{"Re",28.7621,1.67191,15.7189,9.09227,14.5564,0.3505,5.44174,52.0861,10.472},
{"Os",28.1894,1.62903,16.155,8.97948,14.9305,0.382661,5.67589,48.1647,11.0005},
{"Os4+",30.419,1.37113,15.2637,6.84706,14.7458,0.165191,5.06795,18.003,6.49804},
{"Ir",27.3049,1.59279,16.7296,8.86553,15.6115,0.417916,5.83377,45.0011,11.4722},
{"Ir3+",30.4156,1.34323,15.862,7.10909,13.6145,0.204633,5.82008,20.3254,8.27903},
{"Ir4+",30.7058,1.30923,15.5512,6.71983,14.2326,0.167252,5.53672,17.4911,6.96824},
{"Pt",27.0059,1.51293,17.7639,8.81174,15.7131,0.424593,5.7837,38.6103,11.6883},
{"Pt2+",29.8429,1.32927,16.7224,7.38979,13.2153,0.263297,6.35234,22.9426,9.85329},
{"Pt4+",30.9612,1.24813,15.9829,6.60834,13.7348,0.16864,5.92034,16.9392,7.39534},
{"Au",16.8819,0.4611,18.5913,8.6216,25.5582,1.4826,5.86,36.3956,12.0658},
{"Au1+",28.0109,1.35321,17.8204,7.7395,14.3359,0.356752,6.58077,26.4043,11.2299},
{"Au3+",30.6886,1.2199,16.9029,6.82872,12.7801,0.212867,6.52354,18.659,9.0968},
{"Hg",20.6809,0.545,19.0417,8.4484,21.6575,1.5729,5.9676,38.3246,12.6089},
{"Hg1+",25.0853,1.39507,18.4973,7.65105,16.8883,0.443378,6.48216,28.2262,12.0205},
{"Hg2+",29.5641,1.21152,18.06,7.05639,12.8374,0.284738,6.89912,20.7482,10.6268},
{"Tl",27.5446,0.65515,19.1584,8.70751,15.538,1.96347,5.52593,45.8149,13.1746},
{"Tl1+",21.3985,1.4711,20.4723,0.517394,18.7478,7.43463,6.82847,28.8482,12.5258},
{"Tl3+",30.8695,1.1008,18.3481,6.53852,11.9328,0.219074,7.00574,17.2114,9.8027},
{"Pb",31.0617,0.6902,13.0637,2.3576,18.442,8.618,5.9696,47.2579,13.4118},
{"Pb2+",21.7886,1.3366,19.5682,0.488383,19.1406,6.7727,7.01107,23.8132,12.4734},
{"Pb4+",32.1244,1.00566,18.8003,6.10926,12.0175,0.147041,6.96886,14.714,8.08428},
{"Bi",33.3689,0.704,12.951,2.9238,16.5877,8.7937,6.4692,48.0093,13.5782},
{"Bi3+",21.8053,1.2356,19.5026,6.24149,19.1053,0.469999,7.10295,20.3185,12.4711},
{"Bi5+",33.5364,0.91654,25.0946,0.39042,19.2497,5.71414,6.91555,12.8285,-6.7994},
{"Po",34.6726,0.700999,15.4733,3.55078,13.1138,9.55642,7.02588,47.0045,13.677},
{"At",35.3163,0.68587,19.0211,3.97458,9.49887,11.3824,7.42518,45.4715,13.7108},
{"Rn",35.5631,0.6631,21.2816,4.0691,8.0037,14.0422,7.4433,44.2473,13.6905},
{"Fr",35.9299,0.646453,23.0547,4.17619,12.1439,23.1052,2.11253,150.645,13.7247},
{"Ra",35.763,0.616341,22.9064,3.87135,12.4739,19.9887,3.21097,142.325,13.6211},
{"Ra2+",35.215,0.604909,21.67,3.5767,7.91342,12.601,7.65078,29.8436,13.5431},
{"Ac",35.6597,0.589092,23.1032,3.65155,12.5977,18.599,4.08655,117.02,13.5266},
{"Ac3+",35.1736,0.579689,22.1112,3.41437,8.19216,12.9187,7.05545,25.9443,13.4637},
{"Th",35.5645,0.563359,23.4219,3.46204,12.7473,17.8309,4.80703,99.1722,13.4314},
{"Th4+",35.1007,0.555054,22.4418,3.24498,9.78554,13.4661,5.29444,23.9533,13.376},
{"Pa",35.8847,0.547751,23.2948,3.41519,14.1891,16.9235,4.17287,105.251,13.4287},
{"U",36.0228,0.5293,23.4128,3.3253,14.9491,16.0927,4.188,100.613,13.3966},
{"U3+",35.5747,0.52048,22.5259,3.12293,12.2165,12.7148,5.37073,26.3394,13.3092},
{"U4+",35.3715,0.516598,22.5326,3.05053,12.0291,12.5723,4.7984,23.4582,13.2671},
{"U6+",34.8509,0.507079,22.7584,2.8903,14.0099,13.1767,1.21457,25.2017,13.1665},
{"Np",36.1874,0.511929,23.5964,3.25396,15.6402,15.3622,4.1855,97.4908,13.3573},
{"Np3+",35.7074,0.502322,22.613,3.03807,12.9898,12.1449,5.43227,25.4928,13.2544},
{"Np4+",35.5103,0.498626,22.5787,2.96627,12.7766,11.9484,4.92159,22.7502,13.2116},
{"Np6+",35.0136,0.48981,22.7286,2.81099,14.3884,12.33,1.75669,22.6581,13.113},
{"Pu",36.5254,0.499384,23.8083,3.26371,16.7707,14.9455,3.47947,105.98,13.3812},
{"Pu3+",35.84,0.484938,22.7169,2.96118,13.5807,11.5331,5.66016,24.3992,13.1991},
{"Pu4+",35.6493,0.481422,22.646,2.8902,13.3595,11.316,5.18831,21.8301,13.1555},
{"Pu6+",35.1736,0.473204,22.7181,2.73848,14.7635,11.553,2.28678,20.9303,13.0582},
{"Am",36.6706,0.483629,24.0992,3.20647,17.3415,14.3136,3.49331,102.273,13.3592},
{"Cm",36.6488,0.465154,24.4096,3.08997,17.399,13.4346,4.21665,88.4834,13.2887},
{"Bk",36.7881,0.451018,24.7736,3.04619,17.8919,12.8946,4.23284,86.003,13.2754},
{"Cf",36.9185,0.437533,25.1995,3.00775,18.3317,12.4044,4.24391,83.7881,13.2674}
};
#endif
typedef struct At_Bond {
float A1X;
float A1Y;
float A1Z;
int A1AtNb;
float A2X;
float A2Y;
float A2Z;
int A2AtNb;
} At_Bond;
class Atom
{
public:
Atom();
Atom(CString Type, int AtNb, float x, float y, float z);
Atom(CString Type, float x, float y, float z);
Atom(CString Type, CString Label, float x, float y, float z);
Atom(Atom *newAtom);
Atom(CString Type);
~Atom(void);
void RefreshProperties();
//it does nothing
bool GetColor(int Atomic_number, float color[3]);
static CString getAtomType(CString str);
static CString getAtomType(int atnb);
static CString getAtomLabelForCrystals(CString label);
float getFormFactor(float q);
void Rename(int newindex);
int AtomicNumber;
CString AtomType;
CString AtomLabel;
float X;
float Y;
float Z;
bool visible;
ElementDescription ATproperties;
AtomicFormFactor AtFormFactor;
private:
void SetProperties();
};
class bondRestr
{
public:
bondRestr();
~bondRestr();
Atom A1;
Atom A2;
float d;
};
class angleRestr
{
public:
angleRestr();
~angleRestr();
Atom A1;
Atom A2;
Atom A3;
float a;
};
class Molecule
{
public:
Molecule();
Molecule(CString moleculeName);
Molecule(Molecule *newMolecule);
~Molecule();
void AddNewAtom(CString Type, int AtNb, float x, float y, float z);
void AddNewAtom(CString Type, float x, float y, float z);
void AddNewAtom(CString Type, CString label, float x, float y, float z);
void AddNewAtom(Atom At);
void GetCenter(float &x, float &y, float &z);
void UseCentralAtom(int ID);
void UseCenterOfMass();
bool getUse_mass_center();
bool BuildBonds();
void BuildRestr();
int GetAtomNb();
Atom GetAtom(int i);
Atom *GetAtomPointer(int i);
void SetAtom(int i, Atom At);
float Angle(Atom *A, Atom *B, Atom *C);
CString GetMoleculeName();
void Move(float vect[3]);
void Rotate(float rot[3][3]);
void MoveToPoint(float point[3]);
void setOrigID(int ID);
int getOrigID();
void multiplyAtomsByMatrix(float m[3][3]);
void RemoveBondsAndAtoms();
bool isApplySymmetry();
void ApplySymmetry(bool apply=true);
bool isManuallyAdded();
void ManuallyAdded(bool added=true);
std::vector<At_Bond> Bond;
bool visible;
std::vector<bondRestr> brestr;
std::vector<angleRestr> arestr;
private:
void multiplyMatrix(Atom *At, float matrix[3][3]);
void RemoveNumbersFromString(CString &s);
float Distance(float Ax, float Ay, float Az, float Bx, float By, float Bz);
CString Name;
std::vector<Atom> Atoms;
//id of equivalent molecules / fragments
int m_origID;
bool m_use_mass_center;
int m_central_atom;
bool m_apply_symmetry;
bool m_manually_added;
};
typedef struct Zmatrix_unit {
std::string name;
int id_dist;
float dist;
int id_angl;
float angl;
int id_dihedral;
float dihedral;
} Zmatrix_unit;
class ZMatrix
{
public:
ZMatrix();
~ZMatrix();
std::vector<Zmatrix_unit> m_zmatrix;
};
class UnitCell
{
public:
UnitCell(float a, float b, float c, float alpha, float beta, float gama);
UnitCell();
~UnitCell();
void SetSpaceGroup(CString Spcgrp);
void SetSpaceGroupSpecial(CString Spcgrp);//without generating FtCmatrixes;
CString getSpaceGroup();
void SaveToFile(CArchive *ar);
void LoadValues(map<CString,CString> params);
void AddNewAtomInFract(Atom At, int nMolecule = 0, bool apply_symmetry=true, bool manually_added=false);//0,1,2,...,n
void AddNewAtomInFract(CString Type, float x, float y, float z, int nMolecule = 0, bool apply_symmetry=true, bool manually_added=false);//0,1,2,...,n
void AddNewAtomInFract(CString Type, CString label, float x, float y, float z, int nMolecule = 0, bool apply_symmetry=true, bool manually_added=false);//0,1,2,...,n
void generateMoleculesFromAssymPart();
//void AddNewAtomInCart(Atom At, int nMolecule = -1);//0,1,2,...,n
//void AddNewAtomInCart(CString Name, float x, float y, float z, int nMolecule = -1);//0,1,2,...,n
void AddNewCavity(float x, float y, float z, float r, float t=0, CString name="");
void SetQuaternion(float q0, float q1, float q2, float q3);
void MakeQuaternion(float &x, float &y, float &z);
void CalcCartToFract(float &X, float &Y, float &Z);
void CalcFractToCart(float &X, float &Y, float &Z);
void CalcCartToFract(Atom *At);
void CalcFractToCart(Atom *At);
void BuildRestr();
void ClearGeneratedAtoms();
void setFtC_Matrix(float m[3][3]);
void getFTC_Matrix(float m[3][3]);
void getCTF_Matrix(float m[3][3]);
void setShrinkMap(VoxelMap *map, float shrink_dist=0);
void SetToUnitCell(Atom *At);
static bool isBond(Atom *A, Atom *B);
static Atom multiplyMatrix(Atom *At, float matrix[3][4]);
static Atom multiplyMatrix(Atom *At, vector<vector<float>> &matrix);
static float Angle(Atom *A, Atom *B, Atom *C);
static float Distance(float Ax, float Ay, float Az, float Bx, float By, float Bz);
static void InvertMatrix(float m[3][3], float mi[3][3]);
vector<Molecule> getAssym_part_molecule_cart();
vector<Molecule> getAssym_part_molecule_fract();
vector<Molecule> getUnitcell_molecule_cart();
vector<Molecule> *getUnitcell_molecule_cart_pointer();
vector<Molecule> getUnitcell_molecule_fract();
//copy of original atoms
vector<Atom> getAssym_part_atoms_cart();
vector<Atom> getAssym_part_atoms_fract();
//atoms generated by symmetry matrixes
vector<Atom> getUnitcell_atoms_cart();
vector<Atom> getUnitcell_atoms_fract();
//at has to be in fractional coordinates!
std::vector<Atom> getEquivalentPositions(Atom at);
void MoveUnitCellMolecule_cart(int nb, float vector_cart[3]);
void RotateUnitCellMolecule_cart(int nb, float rot[3][3]);
void MoveOriginalMolecule(int origID, float vector_cart[3]);
void MoveOriginalMolecule(int origID, float vector_cart[3], float viewR[4][4]);
void MoveOriginalMoleculeToThePoint(int origID, float point_cart[3]);
void RotateOriginalMolecule(int origID, float rot[3][3]);
void MultiplyOriginalMoleculeByMatrix(int origID, float rot[3][3]);
void RotateOriginalMolecule(int origID, float R[3][3], float viewR[4][4]);
Molecule &getOriginalMolecule(int origID);
void GenerateFractToOrtMatrix();
//void generateBasicMoleculesFromAssymPart();
bool FillInUnitCell();
void BuildCavities();
//void DoMismatch();
/*
int GetMoleculeNb();
Molecule *GetBasicMolecule(int i);
int GetAtomNb();
int GetBonds();
Atom *GetAtom(int i);
*/
Atom GetUnitPoint_cart(int i);
Atom GetUnitPoint_fract(int i);
//void SetAllBasicMoleculesInFract();
//void SetAllBasicMoleculesInCart();
void SetATProperties(ElementDescription properties[], int nb);
CString Name;
bool Option_setToUnitCell;
bool Option_dummy_fill;
bool Option_Organic;
bool isSpaceGroup;
//int nbMatrix;
vector<vector<vector<float>>> listMatrix;
float Translation_Matrix[3];
std::vector<At_Bond> Bond;
//std::vector<Molecule *> UnitMolecule; //for drawing
float A, B, C;
float Alpha, Beta, Gama;//in degrees!!!
vector<MCECavity> UnitCavities;
vector<bondRestr> brestr;
vector<angleRestr> arestr;
private:
void Init();
void SetToUnitCellVector(Atom *At, float *vector);
void BuildBonds();
bool isPosInTheList(Atom at, std::vector<Atom> &list, float spec_pos_lim=0.01);
Atom UnitPoint_cart[8];
Atom UnitPoint_fract[8];
float Q[4];
CString SpaceGroup;
bool isFTC_CTF;
float FtC_Matrix[3][3];
float CtF_Matrix[3][3];
VoxelMap *m_shrink_map;
float m_shrink_dist;
vector<Molecule> m_assym_part_molecule_cart;
vector<Molecule> m_assym_part_molecule_fract;
vector<Molecule> m_unitcell_molecule_cart;
vector<Molecule> m_unitcell_molecule_fract;
//copy of original atoms
vector<Atom> m_assym_part_atoms_cart;
vector<Atom> m_assym_part_atoms_fract;
//atoms generated by symmetry matrixes
vector<Atom> m_unitcell_atoms_cart;
vector<Atom> m_unitcell_atoms_fract;
//std::vector<Molecule> m_original_molecule_cart;
vector<Molecule> m_original_molecule_fract;
//atoms as read from file
//std::vector<Atom> m_original_atoms_cart;
vector<Atom> m_original_atoms_fract;
vector<MCECavity> BasicCavities; //cavities - fract coords
};
