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/***********************************************************************************
LibBQB - File Format and Compression Algorithms for Trajectories of
Volumetric Data and Atom Positions
https://brehm-research.de/bqb
Free software, licensed under GNU LGPL v3
Copyright (c) Martin Brehm and Martin Thomas,
Martin Luther University Halle-Wittenberg, Germany,
2016 - 2020.
Please cite: M. Brehm, M. Thomas: "An Efficient Lossless Compression Algorithm
for Trajectories of Atom Positions and Volumetric Data",
J. Chem. Inf. Model. 2018, 58 (10), pp 2092-2107.
--------------------------------------------------------------------------------
LibBQB is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program 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 Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
***********************************************************************************/
// This must always be the first include directive
#include "bqb_config.h"
#include "bqb_tools.h"
#include <stdarg.h>
#include "bqb_interface.h"
#include "bqb_format.h"
const char *GetRevisionInfo_bqb_tools(unsigned int len) {
static char buf[256];
GET_REVISION_INFO( buf, len );
return buf;
}
const char *GetSourceVersion_bqb_tools() {
static char buf[256];
GET_SOURCE_VERSION( buf );
return buf;
}
int bqb_strcmp_nocase(const char *s1, const char *s2) {
char *buf, *buf2;
unsigned long z;
int i;
buf = new char[strlen(s1)+1];
buf2 = new char[strlen(s2)+1];
for (z=0;z<strlen(s1);z++)
buf[z] = (char)toupper(s1[z]);
buf[strlen(s1)] = 0;
for (z=0;z<strlen(s2);z++)
buf2[z] = (char)toupper(s2[z]);
buf2[strlen(s2)] = 0;
i = strcmp(buf,buf2);
delete[] buf;
delete[] buf2;
return i;
}
void PushNumeration(std::vector<int> &ia, int n, int s1, int s2) {
/* int t, i, z, a;
// printf("Push %d ...\n",n);
t = (int)(floor(mylog2(n+1))+0.5);
// printf("t=%d\n",t);
i = n;
for (z=0;z<t;z++) {
a = i - 2*(((int)(ceil(i/2.0)+0.5)) - 1);
// printf("%d\n",a);
if (a == 1)
ia.push_back(s1);
else
ia.push_back(s2);
i = ((int)(ceil(i/2.0)+0.5)) - 1;
}*/
int z2;
z2 = n-1;
while (true) {
if (z2 & 1)
ia.push_back(s2);
else
ia.push_back(s1);
if (z2 < 2)
break;
z2 = (z2 - 2) / 2;
}
}
int GetAtomOrd(const char *s) {
// First the one-letter labels ...
if (bqb_strcmp_nocase(s, "H" ) == 0) return 1;
if (bqb_strcmp_nocase(s, "D" ) == 0) return 1;
if (bqb_strcmp_nocase(s, "B" ) == 0) return 5;
if (bqb_strcmp_nocase(s, "C" ) == 0) return 6;
if (bqb_strcmp_nocase(s, "N" ) == 0) return 7;
if (bqb_strcmp_nocase(s, "O" ) == 0) return 8;
if (bqb_strcmp_nocase(s, "F" ) == 0) return 9;
if (bqb_strcmp_nocase(s, "P" ) == 0) return 15;
if (bqb_strcmp_nocase(s, "S" ) == 0) return 16;
if (bqb_strcmp_nocase(s, "K" ) == 0) return 19;
if (bqb_strcmp_nocase(s, "V" ) == 0) return 23;
if (bqb_strcmp_nocase(s, "Y" ) == 0) return 39;
if (bqb_strcmp_nocase(s, "I" ) == 0) return 53;
if (bqb_strcmp_nocase(s, "W" ) == 0) return 74;
if (bqb_strcmp_nocase(s, "U" ) == 0) return 92;
// Then the two-letter labels.
if (bqb_strcmp_nocase(s, "He" ) == 0) return 2;
if (bqb_strcmp_nocase(s, "Li" ) == 0) return 3;
if (bqb_strcmp_nocase(s, "Be" ) == 0) return 4;
if (bqb_strcmp_nocase(s, "Ne" ) == 0) return 10;
if (bqb_strcmp_nocase(s, "Na" ) == 0) return 11;
if (bqb_strcmp_nocase(s, "Mg" ) == 0) return 12;
if (bqb_strcmp_nocase(s, "Al" ) == 0) return 13;
if (bqb_strcmp_nocase(s, "Si" ) == 0) return 14;
if (bqb_strcmp_nocase(s, "Cl" ) == 0) return 17;
if (bqb_strcmp_nocase(s, "Ar" ) == 0) return 18;
if (bqb_strcmp_nocase(s, "Ca" ) == 0) return 20;
if (bqb_strcmp_nocase(s, "Sc" ) == 0) return 21;
if (bqb_strcmp_nocase(s, "Ti" ) == 0) return 22;
if (bqb_strcmp_nocase(s, "Cr" ) == 0) return 24;
if (bqb_strcmp_nocase(s, "Mn" ) == 0) return 25;
if (bqb_strcmp_nocase(s, "Fe" ) == 0) return 26;
if (bqb_strcmp_nocase(s, "Co" ) == 0) return 27;
if (bqb_strcmp_nocase(s, "Ni" ) == 0) return 28;
if (bqb_strcmp_nocase(s, "Cu" ) == 0) return 29;
if (bqb_strcmp_nocase(s, "Zn" ) == 0) return 30;
if (bqb_strcmp_nocase(s, "Ga" ) == 0) return 31;
if (bqb_strcmp_nocase(s, "Ge" ) == 0) return 32;
if (bqb_strcmp_nocase(s, "As" ) == 0) return 33;
if (bqb_strcmp_nocase(s, "Se" ) == 0) return 34;
if (bqb_strcmp_nocase(s, "Br" ) == 0) return 35;
if (bqb_strcmp_nocase(s, "Kr" ) == 0) return 36;
if (bqb_strcmp_nocase(s, "Rb" ) == 0) return 37;
if (bqb_strcmp_nocase(s, "Sr" ) == 0) return 38;
if (bqb_strcmp_nocase(s, "Zr" ) == 0) return 40;
if (bqb_strcmp_nocase(s, "Nb" ) == 0) return 41;
if (bqb_strcmp_nocase(s, "Mo" ) == 0) return 42;
if (bqb_strcmp_nocase(s, "Tc" ) == 0) return 43;
if (bqb_strcmp_nocase(s, "Ru" ) == 0) return 44;
if (bqb_strcmp_nocase(s, "Rh" ) == 0) return 45;
if (bqb_strcmp_nocase(s, "Pd" ) == 0) return 46;
if (bqb_strcmp_nocase(s, "Ag" ) == 0) return 47;
if (bqb_strcmp_nocase(s, "Cd" ) == 0) return 48;
if (bqb_strcmp_nocase(s, "In" ) == 0) return 49;
if (bqb_strcmp_nocase(s, "Sn" ) == 0) return 50;
if (bqb_strcmp_nocase(s, "Sb" ) == 0) return 51;
if (bqb_strcmp_nocase(s, "Te" ) == 0) return 52;
if (bqb_strcmp_nocase(s, "Xe" ) == 0) return 54;
if (bqb_strcmp_nocase(s, "Cs" ) == 0) return 55;
if (bqb_strcmp_nocase(s, "Ba" ) == 0) return 56;
if (bqb_strcmp_nocase(s, "La" ) == 0) return 57;
if (bqb_strcmp_nocase(s, "Ce" ) == 0) return 58;
if (bqb_strcmp_nocase(s, "Pr" ) == 0) return 59;
if (bqb_strcmp_nocase(s, "Nd" ) == 0) return 60;
if (bqb_strcmp_nocase(s, "Pm" ) == 0) return 61;
if (bqb_strcmp_nocase(s, "Sm" ) == 0) return 62;
if (bqb_strcmp_nocase(s, "Eu" ) == 0) return 63;
if (bqb_strcmp_nocase(s, "Gd" ) == 0) return 64;
if (bqb_strcmp_nocase(s, "Tb" ) == 0) return 65;
if (bqb_strcmp_nocase(s, "Dy" ) == 0) return 66;
if (bqb_strcmp_nocase(s, "Ho" ) == 0) return 67;
if (bqb_strcmp_nocase(s, "Er" ) == 0) return 68;
if (bqb_strcmp_nocase(s, "Tm" ) == 0) return 69;
if (bqb_strcmp_nocase(s, "Yb" ) == 0) return 70;
if (bqb_strcmp_nocase(s, "Lu" ) == 0) return 71;
if (bqb_strcmp_nocase(s, "Hf" ) == 0) return 72;
if (bqb_strcmp_nocase(s, "Ta" ) == 0) return 73;
if (bqb_strcmp_nocase(s, "Re" ) == 0) return 75;
if (bqb_strcmp_nocase(s, "Os" ) == 0) return 76;
if (bqb_strcmp_nocase(s, "Ir" ) == 0) return 77;
if (bqb_strcmp_nocase(s, "Pt" ) == 0) return 78;
if (bqb_strcmp_nocase(s, "Au" ) == 0) return 79;
if (bqb_strcmp_nocase(s, "Hg" ) == 0) return 80;
if (bqb_strcmp_nocase(s, "Tl" ) == 0) return 81;
if (bqb_strcmp_nocase(s, "Pb" ) == 0) return 82;
if (bqb_strcmp_nocase(s, "Bi" ) == 0) return 83;
if (bqb_strcmp_nocase(s, "Po" ) == 0) return 84;
if (bqb_strcmp_nocase(s, "At" ) == 0) return 85;
if (bqb_strcmp_nocase(s, "Rn" ) == 0) return 86;
if (bqb_strcmp_nocase(s, "Fr" ) == 0) return 87;
if (bqb_strcmp_nocase(s, "Ra" ) == 0) return 88;
if (bqb_strcmp_nocase(s, "Ac" ) == 0) return 89;
if (bqb_strcmp_nocase(s, "Th" ) == 0) return 90;
if (bqb_strcmp_nocase(s, "Pa" ) == 0) return 91;
if (bqb_strcmp_nocase(s, "Np" ) == 0) return 93;
if (bqb_strcmp_nocase(s, "Pu" ) == 0) return 94;
if (bqb_strcmp_nocase(s, "Am" ) == 0) return 95;
if (bqb_strcmp_nocase(s, "Cm" ) == 0) return 96;
if (bqb_strcmp_nocase(s, "Bk" ) == 0) return 97;
if (bqb_strcmp_nocase(s, "Cf" ) == 0) return 98;
if (bqb_strcmp_nocase(s, "Es" ) == 0) return 99;
if (bqb_strcmp_nocase(s, "Fm" ) == 0) return 100;
if (bqb_strcmp_nocase(s, "Md" ) == 0) return 101;
if (bqb_strcmp_nocase(s, "No" ) == 0) return 102;
if (bqb_strcmp_nocase(s, "Lr" ) == 0) return 103;
return 200;
}
const char* GetAtomOrdLabel( int ord ) {
switch( ord ) {
case 1: return "H" ;
case 2: return "He";
case 3: return "Li";
case 4: return "Be";
case 5: return "B" ;
case 6: return "C" ;
case 7: return "N" ;
case 8: return "O" ;
case 9: return "F" ;
case 10: return "Ne";
case 11: return "Na";
case 12: return "Mg";
case 13: return "Al";
case 14: return "Si";
case 15: return "P" ;
case 16: return "S" ;
case 17: return "Cl";
case 18: return "Ar";
case 19: return "K" ;
case 20: return "Ca";
case 21: return "Sc";
case 22: return "Ti";
case 23: return "V" ;
case 24: return "Cr";
case 25: return "Mn";
case 26: return "Fe";
case 27: return "Co";
case 28: return "Ni";
case 29: return "Cu";
case 30: return "Zn";
case 31: return "Ga";
case 32: return "Ge";
case 33: return "As";
case 34: return "Se";
case 35: return "Br";
case 36: return "Kr";
case 37: return "Rb";
case 38: return "Sr";
case 39: return "Y" ;
case 40: return "Zr";
case 41: return "Nb";
case 42: return "Mo";
case 43: return "Tc";
case 44: return "Ru";
case 45: return "Rh";
case 46: return "Pd";
case 47: return "Ag";
case 48: return "Cd";
case 49: return "In";
case 50: return "Sn";
case 51: return "Sb";
case 52: return "Te";
case 53: return "I" ;
case 54: return "Xe";
case 55: return "Cs";
case 56: return "Ba";
case 57: return "La";
case 58: return "Ce";
case 59: return "Pr";
case 60: return "Nd";
case 61: return "Pm";
case 62: return "Sm";
case 63: return "Eu";
case 64: return "Gd";
case 65: return "Tb";
case 66: return "Dy";
case 67: return "Ho";
case 68: return "Er";
case 69: return "Tm";
case 70: return "Yb";
case 71: return "Lu";
case 72: return "Hf";
case 73: return "Ta";
case 74: return "W" ;
case 75: return "Re";
case 76: return "Os";
case 77: return "Ir";
case 78: return "Pt";
case 79: return "Au";
case 80: return "Hg";
case 81: return "Tl";
case 82: return "Pb";
case 83: return "Bi";
case 84: return "Po";
case 85: return "At";
case 86: return "Rn";
case 87: return "Fr";
case 88: return "Ra";
case 89: return "Ac";
case 90: return "Th";
case 91: return "Pa";
case 92: return "U" ;
case 93: return "Np";
case 94: return "Pu";
case 95: return "Am";
case 96: return "Cm";
case 97: return "Bk";
case 98: return "Cf";
case 99: return "Es";
case 100: return "Fm";
case 101: return "Md";
case 102: return "No";
case 103: return "Lr";
}
return "X";
}
bool BQBFileExist(const char *s) {
FILE *a;
a = fopen(s,"rb");
if (a == NULL)
return false;
fclose(a);
return true;
}
FILE* CBQBTools::BQBOpenFileWrite(const char *buf, bool text) {
FILE *a;
if (text)
a = fopen(buf,"wt");
else
a = fopen(buf,"wb");
if (a == NULL) {
m_IF.eprintf("Could not open file \"%s\" for writing.\nBe sure to have writing permission for this directory.\n\nAborting execution.\n",buf);
abort();
}
return a;
}
long CBQBTools::FindIndexPosition(FILE *a) {
unsigned int i;
unsigned char uc;
long l;
char buf[3];
if (m_IF.IsPL(BQB_PL_DEBUG))
m_IF.printf(">>> FindIndexPosition >>>\n");
if (a == NULL) {
if (m_IF.IsPL(BQB_PL_DEBUG)) {
m_IF.printf(" File pointer == NULL.\n");
m_IF.printf("<<< FindIndexPosition <<<\n\n");
}
return 0;
}
fseek(a,-3,SEEK_END);
(void)fread(buf,3,1,a);
// if (memcmp(buf,"IDX",3) != 0) {
if ((buf[0] != 'I') || (buf[1] != 'D') || (buf[2] != 'X')) { // To prevent Valgrind "uninitialized value" warning
if (m_IF.IsPL(BQB_PL_DEBUG)) {
m_IF.printf(" Last three characters differ from \"IDX\".\n");
m_IF.printf("<<< FindIndexPosition <<<\n\n");
}
return 0;
} else if (m_IF.IsPL(BQB_PL_DEBUG))
m_IF.printf(" Found \"IDX\".\n");
fseek(a,-7,SEEK_END);
(void)fread(&uc,1,1,a);
i = ((unsigned int)uc) << 24;
(void)fread(&uc,1,1,a);
i += ((unsigned int)uc) << 16;
(void)fread(&uc,1,1,a);
i += ((unsigned int)uc) << 8;
(void)fread(&uc,1,1,a);
i += uc;
if (m_IF.IsPL(BQB_PL_DEBUG))
m_IF.printf(" Found index frame length %u.\n",i);
fseek(a,-((int)i),SEEK_END);
l = ftell(a);
if (m_IF.IsPL(BQB_PL_DEBUG)) {
m_IF.printf(" Found index frame offset %ld.\n",l);
m_IF.printf("<<< FindIndexPosition <<<\n\n");
}
return l;
}
void BQBFormatTime(unsigned long eta, char *buf) {
char tbuf[256], tbuf2[256];
if (buf == NULL)
return;
if ((eta/60) > 0)
sprintf(tbuf,"%02lus",eta%60);
else
sprintf(tbuf,"%2lus",eta%60);
eta /= 60;
if (eta > 0) {
strcpy(tbuf2,tbuf);
if ((eta/60) > 0)
sprintf(tbuf,"%02lum",eta%60);
else
sprintf(tbuf,"%2lum",eta%60);
strcat(tbuf,tbuf2);
eta /= 60;
if (eta > 0) {
strcpy(tbuf2,tbuf);
if ((eta/60) > 0)
sprintf(tbuf,"%02luh",eta%24);
else
sprintf(tbuf,"%2luh",eta%24);
strcat(tbuf,tbuf2);
eta /= 24;
}
if (eta > 0) {
strcpy(tbuf2,tbuf);
if ((eta/60) > 0)
sprintf(tbuf,"%02lud",eta);
else
sprintf(tbuf,"%2lud",eta);
strcat(tbuf,tbuf2);
}
}
strcpy(buf,tbuf);
}
bool bqbisinteger(const char *s) {
int z;
z = 0;
if (strlen(s) > 0)
if (s[0] == '-')
z++;
for (;z<(int)strlen(s);z++)
if ((s[z] < 0) || (s[z] > 9))
return false;
return true;
}
void CBQBStatistics::PushStatistics() {
m_oaStatStack.push_back(m_oStat);
}
void CBQBStatistics::PopStatistics() {
if (m_oaStatStack.size() == 0) {
m_IF.eprintf("CBQBStatistics::PopStatistics(): Error: Statistics stack is empty.\n");
abort();
}
m_oStat.m_lSize = m_oaStatStack.back().m_lSize;
m_oStat.m_lOverhead = m_oaStatStack.back().m_lOverhead;
m_oStat.m_lAlphabet = m_oaStatStack.back().m_lAlphabet;
m_oStat.m_lHuffmanTables = m_oaStatStack.back().m_lHuffmanTables;
m_oStat.m_lTableSwitch = m_oaStatStack.back().m_lTableSwitch;
m_oStat.m_lHuffmanData = m_oaStatStack.back().m_lHuffmanData;
m_oaStatStack.pop_back();
}
void CBQBStatistics::PopDiffStatistics() {
if (m_oaStatStack.size() < 2) {
m_IF.eprintf("CBQBStatistics::PopDiffStatistics(): Error: Statistics stack has size of %lu < 2.\n",m_oaStatStack.size());
abort();
}
m_oStat.m_lSize += m_oaStatStack[m_oaStatStack.size()-2].m_lSize - m_oaStatStack.back().m_lSize;
m_oStat.m_lOverhead += m_oaStatStack[m_oaStatStack.size()-2].m_lOverhead - m_oaStatStack.back().m_lOverhead;
m_oStat.m_lAlphabet += m_oaStatStack[m_oaStatStack.size()-2].m_lAlphabet - m_oaStatStack.back().m_lAlphabet;
m_oStat.m_lHuffmanTables += m_oaStatStack[m_oaStatStack.size()-2].m_lHuffmanTables - m_oaStatStack.back().m_lHuffmanTables;
m_oStat.m_lTableSwitch += m_oaStatStack[m_oaStatStack.size()-2].m_lTableSwitch - m_oaStatStack.back().m_lTableSwitch;
m_oStat.m_lHuffmanData += m_oaStatStack[m_oaStatStack.size()-2].m_lHuffmanData - m_oaStatStack.back().m_lHuffmanData;
m_oaStatStack.pop_back();
}
void CBQBStatistics::ResetStatistics() {
m_oaStatStack.clear();
m_oStat.reset();
}
void CBQBStatistics::PopIgnoreStatistics() {
if (m_oaStatStack.size() == 0) {
m_IF.eprintf("CBQBStatistics::PopStatistics(): Error: Statistics stack is empty.\n");
abort();
}
m_oaStatStack.pop_back();
}
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