void LuminesRobot::thinkNextBlock(btype *map, int width, int height, const BlockSet coming[3])
{
int i, j;
::std::vector< int > tops(width,0);
::std::vector< Sets > sets((width-1)*4*(width-1)*4*(width-1)*4);
sets.clear();
tops.clear();
for (i=0;i<width;i++)
{
for (j=height-1;j>=0;j--)
{
if (map[i+j*width] == BT_NONE)
break;
}
tops.push_back(j);
}
Sets base;
base.level = -1;
thinkNextBlockI(base, tops, sets, 0, map, width, height, coming);
assert(sets.size());
::std::sort(sets.begin(), sets.end());
m_res.clear();
LuRobotResultPair res;
for (i = 0; i <= sets[0].level; i++)
{
res.x = sets[0].x[i];
res.r = sets[0].r[i];
m_res.push_back(res);
}
}
//=============================================================================
// METHOD : SPELLcontroller::notifyCommandToCore
//=============================================================================
void SPELLcontroller::notifyCommandToCore( const std::string& id )
{
// Notify the adapter and the driver to give the chance
// to abort ongoing operations if needed
if (id == CMD_ABORT ||
id == CMD_PAUSE ||
id == CMD_INTERRUPT ||
id == CMD_SKIP ||
id == CMD_RUN)
{
bool controlled = SPELLexecutor::instance().getConfiguration().hasControlClient();
if (controlled)
{
DEBUG("[C] Notify command " + id + " to core IN");
SPELLdriverManager::instance().onCommand(id);
DEBUG("[C] Notify command to core OUT");
}
else
{
DEBUG("[C] Notify command " + id + " to core IN (NOCLT)");
SPELLsafeThreadOperations tops("SPELLcontroller::onCommand()");
SPELLdriverManager::instance().onCommand(id);
DEBUG("[C] Notify command to core OUT");
}
}
}
int main(){
int i;
printf("is stack empty? \n");
printf(BOOL_PRINT(isEmpty()));
push(10);
printf("top is at %d\n",tops() );
push(11);
push(12);
push(15);
i = pop();
printf("Popped data is %d\n",i );
printf("top is at %d\n",tops());
stack_print(); // Note: this is just for vizualizing and this actually results in loss of stack data
return 0;
}
void LuminesRobot::think(btype *map, int width, int height, const BlockSet coming[3])
{
thinkNextBlock(map, width, height, coming);
return;
int i, j;
int r, t;
int score;
BlockSet bs;
int top1, top2;
LuRobotResultPair res;
::std::vector< int > tops(width,0);
::std::vector< Set > sets((width-1)*4);
sets.clear();
tops.clear();
#ifdef _DEBUG
OutputDebugString("\n");
#endif
for (i=0;i<width;i++)
{
for (j=height-1;j>=0;j--)
{
if (map[i+j*width] == BT_NONE)
break;
#ifdef _DEBUG
if (map[i+j*width] == BT_A)
OutputDebugString("a");
else
OutputDebugString("b");
}
char n[3];
sprintf(n,"%d\n",j);
OutputDebugString(n);
#else
}
#endif
tops.push_back(j);
}
/* VARARGS */
char *
tparm(char *instring, long fp1, long fp2, long p3, long p4,
long p5, long p6, long p7, long p8, long p9)
{
static char result[512];
static char added[100];
long vars[26];
STACK stk;
char *cp = instring;
char *outp = result;
char c;
long op;
long op2;
int sign;
int onrow = 0;
long p1 = fp1, p2 = fp2; /* copy in case < 2 actual parms */
char *xp;
char formatbuffer[100];
char *format;
int looping;
short *regs = cur_term->_regs;
int val;
if ((val = setjmp(env)) != 0) {
#ifdef DEBUG
switch (val) {
case MEM_ALLOC_FAIL:
fprintf(outf, "TPARM: Memory allocation"
" failure.");
break;
case STACK_UNDERFLOW:
fprintf(outf, "TPARM: Stack underflow.");
break;
}
#endif /* DEBUG */
if (val == STACK_UNDERFLOW)
free_stack(&stk);
return (NULL);
}
init_stack(&stk);
push(&stk, 0);
if (instring == 0) {
#ifdef DEBUG
if (outf)
fprintf(outf, "TPARM: null arg\n");
#endif /* DEBUG */
free_stack(&stk);
return (NULL);
}
added[0] = 0;
while ((c = *cp++) != 0) {
if (c != '%') {
*outp++ = c;
continue;
}
op = tops(&stk);
switch (c = *cp++) {
/* PRINTING CASES */
case ':':
case ' ':
case '#':
case '0':
case '1':
case '2':
case '3':
case '4':
case '5':
case '6':
case '7':
case '8':
case '9':
case '.':
case 'd':
case 's':
case 'o':
case 'x':
case 'X':
format = formatbuffer;
*format++ = '%';
/* leading ':' to allow +/- in format */
if (c == ':')
c = *cp++;
/* take care of flags, width and precision */
looping = 1;
while (c && looping)
switch (c) {
case '-':
case '+':
case ' ':
case '#':
case '0':
case '1':
case '2':
case '3':
case '4':
case '5':
case '6':
case '7':
case '8':
case '9':
case '.':
*format++ = c;
c = *cp++;
break;
default:
looping = 0;
}
/* add in the conversion type */
switch (c) {
case 'd':
case 's':
case 'o':
case 'x':
case 'X':
*format++ = c;
break;
default:
#ifdef DEBUG
if (outf)
fprintf(outf, "TPARM: invalid "
"conversion type\n");
#endif /* DEBUG */
free_stack(&stk);
return (NULL);
}
*format = '\0';
/*
* Pass off the dirty work to sprintf.
* It's debatable whether we should just pull in
* the appropriate code here. I decided not to for
* now.
*/
if (c == 's')
(void) sprintf(outp, formatbuffer,
(char *) op);
else
(void) sprintf(outp, formatbuffer, op);
/*
* Advance outp past what sprintf just did.
* sprintf returns an indication of its length on some
* systems, others the first char, and there's
* no easy way to tell which. The Sys V on
* BSD emulations are particularly confusing.
*/
while (*outp)
outp++;
(void) pop(&stk);
continue;
case 'c':
/*
* This code is worth scratching your head at for a
* while. The idea is that various weird things can
* happen to nulls, EOT's, tabs, and newlines by the
* tty driver, arpanet, and so on, so we don't send
* them if we can help it. So we instead alter the
* place being addessed and then move the cursor
* locally using UP or RIGHT.
*
* This is a kludge, clearly. It loses if the
* parameterized string isn't addressing the cursor
* (but hopefully that is all that %c terminals do
* with parms). Also, since tab and newline happen
* to be next to each other in ASCII, if tab were
* included a loop would be needed. Finally, note
* that lots of other processing is done here, so
* this hack won't always work (e.g. the Ann Arbor
* 4080, which uses %B and then %c.)
*/
switch (op) {
/*
* Null. Problem is that our
* output is, by convention, null terminated.
*/
case 0:
op = 0200; /* Parity should */
/* be ignored. */
break;
/*
* Control D. Problem is that certain very
* ancient hardware hangs up on this, so the
* current(!) UNIX tty driver doesn't xmit
* control D's.
*/
case _CHCTRL('d'):
/*
* Newline. Problem is that UNIX will expand
* this to CRLF.
*/
case '\n':
xp = (onrow ? cursor_down :
cursor_right);
if (onrow && xp && op < lines-1 &&
cursor_up) {
op += 2;
xp = cursor_up;
}
if (xp && instring ==
cursor_address) {
(void) strcat(added, xp);
op--;
}
break;
/*
* Tab used to be in this group too,
* because UNIX might expand it to blanks.
* We now require that this tab mode be turned
* off by any program using this routine,
* or using termcap in general, since some
* terminals use tab for other stuff, like
* nondestructive space. (Filters like ul
* or vcrt will lose, since they can't stty.)
* Tab was taken out to get the Ann Arbor
* 4080 to work.
*/
}
/* LINTED */
*outp++ = (char)op;
(void) pop(&stk);
break;
case 'l':
xp = pop_char_p(&stk);
push(&stk, strlen(xp));
break;
case '%':
*outp++ = c;
break;
/*
* %i: shorthand for increment first two parms.
* Useful for terminals that start numbering from
* one instead of zero(like ANSI terminals).
*/
case 'i':
p1++;
p2++;
break;
/* %pi: push the ith parameter */
case 'p':
switch (c = *cp++) {
case '1':
push(&stk, p1);
break;
case '2':
push(&stk, p2);
break;
case '3':
push(&stk, p3);
break;
case '4':
push(&stk, p4);
break;
case '5':
push(&stk, p5);
break;
case '6':
push(&stk, p6);
break;
case '7':
push(&stk, p7);
break;
case '8':
push(&stk, p8);
break;
case '9':
push(&stk, p9);
break;
default:
#ifdef DEBUG
if (outf)
fprintf(outf, "TPARM:"
" bad parm"
" number\n");
#endif /* DEBUG */
free_stack(&stk);
return (NULL);
}
onrow = (c == '1');
break;
/* %Pi: pop from stack into variable i (a-z) */
case 'P':
if (*cp >= 'a' && *cp <= 'z') {
vars[*cp++ - 'a'] = pop(&stk);
} else {
if (*cp >= 'A' && *cp <= 'Z') {
regs[*cp++ - 'A'] =
/* LINTED */
(short) pop(&stk);
}
#ifdef DEBUG
else if (outf) {
fprintf(outf, "TPARM: bad"
" register name\n");
}
#endif /* DEBUG */
}
break;
/* %gi: push variable i (a-z) */
case 'g':
if (*cp >= 'a' && *cp <= 'z') {
push(&stk, vars[*cp++ - 'a']);
} else {
if (*cp >= 'A' && *cp <= 'Z') {
push(&stk, regs[*cp++ - 'A']);
}
#ifdef DEBUG
else if (outf) {
fprintf(outf, "TPARM: bad"
" register name\n");
}
#endif /* DEBUG */
}
break;
/* %'c' : character constant */
case '\'':
push(&stk, *cp++);
if (*cp++ != '\'') {
#ifdef DEBUG
if (outf)
fprintf(outf, "TPARM: missing"
" closing quote\n");
#endif /* DEBUG */
free_stack(&stk);
return (NULL);
}
break;
/* %{nn} : integer constant. */
case '{':
op = 0;
sign = 1;
if (*cp == '-') {
sign = -1;
cp++;
} else
if (*cp == '+')
cp++;
while ((c = *cp++) >= '0' && c <= '9') {
op = 10 * op + c - '0';
}
if (c != '}') {
#ifdef DEBUG
if (outf)
fprintf(outf, "TPARM: missing "
"closing brace\n");
#endif /* DEBUG */
free_stack(&stk);
return (NULL);
}
push(&stk, (sign * op));
break;
/* binary operators */
case '+':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op + op2));
break;
case '-':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op - op2));
break;
case '*':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op * op2));
break;
case '/':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op / op2));
break;
case 'm':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op % op2));
break; /* %m: mod */
case '&':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op & op2));
break;
case '|':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op | op2));
break;
case '^':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op ^ op2));
break;
case '=':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op == op2));
break;
case '>':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op > op2));
break;
case '<':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op < op2));
break;
case 'A':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op && op2));
break; /* AND */
case 'O':
op2 = pop(&stk);
op = pop(&stk);
push(&stk, (op || op2));
break; /* OR */
/* Unary operators. */
case '!':
push(&stk, !pop(&stk));
break;
case '~':
push(&stk, ~pop(&stk));
break;
/* Sorry, no unary minus, because minus is binary. */
/*
* If-then-else. Implemented by a low level hack of
* skipping forward until the match is found, counting
* nested if-then-elses.
*/
case '?': /* IF - just a marker */
break;
case 't': /* THEN - branch if false */
if (!pop(&stk))
cp = _branchto(cp, 'e');
break;
case 'e': /* ELSE - branch to ENDIF */
cp = _branchto(cp, ';');
break;
case ';': /* ENDIF - just a marker */
break;
default:
#ifdef DEBUG
if (outf)
fprintf(outf, "TPARM: bad % "
"sequence\n");
#endif /* DEBUG */
free_stack(&stk);
return (NULL);
}
}
(void) strcpy(outp, added);
free_stack(&stk);
return (result);
}
void CSite::writeSite(const int& iisitsf)
{
//---------------------------------------------------------------------------------------------//
bool isita = bAtomInSite, isiti = bSaltInSite, isitmd = bMDInSite, isitpot = bPotentialInSite,
isitx = bAtomCoordInSite, isitq = bCrgInSite, isitf = bFieldInSite, isitp = bGridPotentialInSite,
isitr = bReactPotentialInSite, isitc = bCoulombPotentialInSite, isitap = bAtomPotentialInSite, isitdeb = bDebyeFractionInSite,
isitsf = bSurfCrgInSite, isittf = bTotalForceInSite, isitrf = bReactForceInSite, isitt = bTotalPotentialInSite,
isitcf = bCoulombForceInSite, iself = bPDB2FRCInSite;
//----- ifrm is true if ANY of the flags for special output have been set
bool ifrm = isita || isitq || isitp || isitf || isitr || isitt || isitc || isitx || isiti || isitrf || isitcf || isitap ||
isittf || isitdeb;
bool isitmp1 = ifrm; ifrm = ifrm || isitsf;
bool ofrm = true;
if (isitmd || isitpot) {iFrcFormatOut = -1; ofrm = false;}
if (!ifrm && (0 == iFrcFormatOut || 3 == iFrcFormatOut))
{
isitx = true; isitq = true; isitf = true; isitp = true;
}
switch (iFrcFormatOut)
{
case 1: isitx = true; isitq = true; isitr = true; isitc = true; break;
case 2: isitx = true; isitq = true; isitr = true; break;
case 3: ofrm = false; break;
}
string vrow(80,' '),datum(65,' '); int j = 0, k = 0;
if (isita)
{
vrow.replace(j,15,"ATOM DESCRIPTOR"); datum.replace(k,5,"ATOM ");
j += 20; k += 5;
}
if (isitx)
{
vrow.replace(j+4,24,"ATOM COORDINATES (X,Y,Z)"); datum.replace(k,12,"COORDINATES ");
j += 30; k += 12;
}
if (isitq)
{
vrow.replace(j+3,6,"CHARGE"); datum.replace(k,7,"CHARGE ");
j += 10; k += 7;
}
if (isitp)
{
vrow.replace(j+2,8,"GRID PT."); datum.replace(k,11,"POTENTIALS ");
j += 10; k += 11;
}
if (isiti)
{
vrow.replace(j+1,8,"SALT CON"); datum.replace(k,5,"SALT ");
j += 10; k += 5;
}
if (80 <= j)
{
isitr = false; isitc = false; isitap = false; isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitr)
{
vrow.replace(j,10," REAC. PT."); datum.replace(k,9,"REACTION ");
j += 10; k += 9;
}
if (80 <= j)
{
isitc = false; isitap = false; isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitc)
{
vrow.replace(j,10," COUL. POT"); datum.replace(k,10,"COULOMBIC ");
j += 10; k += 10;
}
if (80 <= j)
{
isitap = false; isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitap)
{
vrow.replace(j+2,8,"ATOM PT."); datum.replace(k,11,"ATOMIC PT. ");
j += 10; k += 11;
}
if (80 <= j)
{
isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitdeb)
{
vrow.replace(j+3,11,"DEBFRACTION"); datum.replace(k,12,"DEBFRACTION ");
j += 14; k += 12;
}
if (60 <= j)
{
isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitf)
{
vrow.replace(j+4,25,"GRID FIELDS: (Ex, Ey, Ez)"); datum.replace(k,7,"FIELDS ");
j += 30;
}
if (60 <= j)
{
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitrf)
{
vrow.replace(j+4,25,"REAC. FORCE: (Rx, Ry, Rz)"); datum.replace(k,7,"RFORCE ");
j += 30;
}
if (60 <= j)
{
isitsf = false; isittf = false; isitcf = false; isitt = false;
}
if (isitcf)
{
vrow.replace(j+4,25,"COUL. FORCE: (Cx, Cy, Cz)"); datum.replace(k,7,"CFORCE ");
j += 30;
}
if (60 <= j)
{
isitsf = false; isittf = false; isitt = false;
}
if (isittf)
{
vrow.replace(j+4,25,"TOTAL FORCE: (Tx, Ty, Tz)"); datum.replace(k,7,"TFORCE ");
j += 30;
}
if (70 <= j)
{
isitt = false;
}
if (isitt)
{
vrow.replace(j+4,6," TOTAL"); datum.replace(k,6,"TOTAL ");
j += 10;
}
if (50 <= j) isitsf = false;
if (isitsf)
{
vrow.replace(j+4,65,"sCharge, x y z urf.E°n,surf. E[kT/(qA)]");
datum.replace(k,35,"SCh, x, y, z, surf En, surf. E");
j += 50;
}
//---------------------------------------------------------------------------------------------//
/*
* if site potentials required and unformatted read/write, skip during formatted frc file read/write can write unformatted frc.pdb
*/
bool ifrm2 = false, iqass = true;
ifstream ifFileStream;
vector<bool> residsf(iResidueNum,false);
if (!(isitmd || isitpot)) cout << "\nwriting potentials at given sites...\n";
if (iself)
{
cout << "using the current pdb file\n";
ifrm2 = true; iqass = false;
}
else
{
if (!isitpot)
{
ifFileStream.open(strFrciFile.c_str()); // just inquire whether the file exists or not
if (!ifFileStream.is_open())
{
CUnknownInFrcFile warning(strFrciFile);
ifFileStream.close();
return;
}
else
{
cout << "coordinates, etc for potential output read from file " << strFrciFile << endl;
ifrm2 = checkFileFormat(strFrciFile);
}
ifFileStream.close();
}
}
//----- if unformatted may not contain all the info needed for all options, i.e atom info
if (!ifrm2 && isita)
{
CNoAtomInfo warning(strFrciFile);
isita = false; iqass = false;
}
if (!ifrm2) iqass = false;
if (!iself && !isitpot)
{
if (ifrm2) ifFileStream.open(strFrciFile.c_str());
else ifFileStream.open(strFrciFile.c_str(),ios::binary);
if (!ifFileStream.is_open()) CUnknownInFrcFile warning(strFrciFile);
}
if (isitsf) //----- isitsf assumes ifrm2=.true.
{
ifstream ifFileStream15;
string strLine,strHead;
int iresnum;
ifFileStream15.open(strFrciFile.c_str()); // just inquire whether the file exists or not
if (!ifFileStream15.is_open())
{
CUnknownInFrcFile warning(strFrciFile);
}
else
{
cout << "coordinates, etc for potential output read from file " << strFrciFile << endl;
while (!ifFileStream15.eof()) // loop D302
{
getline(ifFileStream15,strLine);
strHead = strLine.substr(0,6);
if (0 != strHead.compare(" ")) strHead = toUpperCase(strHead);
if (0 != strHead.compare("ATOM ") && 0 != strHead.compare("HETATM")) continue;
iresnum = atoi(strLine.substr(23,4).c_str());
residsf[iresnum-1] = true;
}
}
ifFileStream15.close();
}
//---------------------------------------------------------------------------------------------//
ofstream ofFileStream;
if (ofrm) ofFileStream.open(strFrcFile.c_str());
if(!(ofrm || isitmd || isitpot)) ofFileStream.open(strFrcFile.c_str(),ios::binary);
if (!isitmd && !isitpot) cout << "potentials written to file " << strFrcFile << endl << endl;
if (ofrm)
{
ofFileStream << "DELPHI SITE POTENTIAL FILE\n";
ofFileStream << "grid size,percent fill: " << iGrid << " " << fPercentageFill << endl;
ofFileStream << "outer diel. and first one assigned : " << fExDielec << " " << vctfMediaEps[1]*fEPKT << endl;
ofFileStream << "ionic strength (M): " << fIonStrength << endl;
ofFileStream << "ion excl., probe radii: " << fIonRadius << " " << rgfProbeRadius[0] << " " << rgfProbeRadius[1] << endl;
ofFileStream << "linear, nolinear iterations: " << iLinIterateNum << " " << iNonIterateNum << endl;
ofFileStream << "boundary condition: " << iBndyType << endl;
ofFileStream << "Data Output: " << datum << endl;
ofFileStream << "title: " << rgcFileMap << endl;
ofFileStream << "\n\n";
ofFileStream << vrow << endl;
}
if (!ofrm && (!(isitmd || isitpot)))
{
ofFileStream << fixed << setprecision(4);
string strLine;
strLine = "DELPHI FRC FILE"; ofFileStream << strLine << endl;
strLine = "FORMAT NUMBER=1"; ofFileStream << strLine << endl;
strLine = "DATA="; strLine.append(datum); ofFileStream << strLine << endl;
ofFileStream << setw(5) << right << iGrid << setw(10) << right << fPercentageFill << setw(10) << right << fExDielec
<< setw(10) << right << fIonStrength << endl;
for (int i = 1; i <= iMediaNum; i++)
ofFileStream << "dielectric in medium nr. " << i << ": " << vctfMediaEps[i]*fEPKT << endl;
ofFileStream << setw(10) << right << fIonRadius << setw(10) << right << rgfProbeRadius[0] << setw(10) << right << rgfProbeRadius[1]
<< setw(5) << right << iLinIterateNum << setw(5) << right << iNonIterateNum << setw(5) << right << iBndyType << endl;
ofFileStream.unsetf(ios_base::floatfield);
}
if (!iself && (isitrf || isitmd || isittf))
{
CCalcReactForceError warning;
isitrf = false; isittf = false; isitmd = false;
}
vector< SGrid<real> > rfield;
if (isitrf || isitmd || isittf)
{
if (1 == iMediaNum && fZero > abs(vctfMediaEps[1]*fEPKT-1.0))
rfield = rforceeps1();
else
rfield = rforce();
}
//---------------------------------------------------------------------------------------------//
integer nnatom,inum,ncrgs;
SGrid<real> cxyz = {0.0,0.0,0.0},xo,xn,fu,fl,xo2,fxyz,vtemp,xu2,xu,rxyz;
real chrgv,radu,goff,vphi,aphi,etot,phiv,temp,phii,debyefraction,phirt,phict,phir,phias,tcrgs,dist,phirtt,crgs,phiat,phic,phiac,eps,phiact,phit;
real sdist,ff,fn;
string atm,res,rnum,chn,crdstr,atnum,atdes(16,' '),strLine,strHead;
bool isitmp;
int iFound,iresnum,idist,ncrg,jtmp;
vector<bool> atmsf(iAtomNum*iisitsf,false);
vector<real> sold,scomp;
char otemp[10];
string oline(80,' ');
nnatom = 0; chrgv = 0.0; goff = ((real)iGrid+1.0)/2.0; etot = 0.0; phirt = 0.0; phict =0.0;
if (isitpot)
{
CSitePhiError warning;
}
else
{
do // beginning of the big loop on natom
{
if(iself)
{
if (iAtomNum == nnatom) break;
xo = prgfgAtomCoordA[nnatom];
chrgv = vctapAtomPdb[nnatom].getCharge();
radu = vctapAtomPdb[nnatom].getRadius()*fScale;
atm = vctapAtomPdb[nnatom].getAtInf().substr(0,4);
res = vctapAtomPdb[nnatom].getAtInf().substr(6,3);
rnum = vctapAtomPdb[nnatom].getAtInf().substr(11,4);
chn = vctapAtomPdb[nnatom].getAtInf().substr(10,1);
}
else
{
//if (!ifFileStream.is_open()) break;
if(ifrm2) // formatted reading
{
getline(ifFileStream,strLine);
if (ifFileStream.eof()) break;
strHead = strLine.substr(0,6); strHead = toUpperCase(strHead);
if (0 != strHead.compare("ATOM ") && 0 != strHead.compare("HETATM")) continue;
crdstr = strLine.substr(30,24);
atnum = strLine.substr(6,5);
xo.nX = atof(crdstr.substr(0,8).c_str()); xo.nY = atof(crdstr.substr(8,8).c_str()); xo.nZ = atof(crdstr.substr(16,8).c_str());
inum = atoi(atnum.c_str());
}
else // unformatted (binary) reading
{
ifFileStream.read( reinterpret_cast<char*>(&xo.nX),sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&xo.nY),sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&xo.nZ),sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&radu), sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&chrgv),sizeof(real) );
}
} //----- end of atom reading
nnatom++;
isitmp = (isitq && iqass) || isitap || isitp;
if((isita || isitmp) && !iself)
{
atm = strLine.substr(11,5);
res = strLine.substr(17,3);
rnum = strLine.substr(22,4);
chn = strLine.substr(21,1);
if (0 != atm.compare(" ")) {atm = removeSpace(atm); atm = toUpperCase(atm);}
if (0 != res.compare(" ")) {res = removeSpace(res); res = toUpperCase(res);}
if (0 != rnum.compare(" ")) {rnum = removeSpace(rnum); rnum = toUpperCase(rnum);}
if (0 != chn.compare(" ")) {chn = removeSpace(chn); chn = toUpperCase(chn);}
}
xn = (xo-fgBoxCenter)*fScale+goff; // scale atoms to grid space
if (isita)
{
atdes.assign(16,' ');
atdes.replace( 0,atm.size(),atm);
atdes.replace( 5,res.size(),res);
atdes.replace( 9,chn.size(),chn);
atdes.replace(11,rnum.size(),rnum);
}
/*
* assign charge to atom, searching for decreasingly specific specification
* note if no charge record found, is assumed to be 0.0
*/
if(!iself && ifrm2 && isitmp)
{
chrgv = 0.0;
iFound = FindRecord(atm,res,rnum,chn,CHARGEFILE,chrgv);
if(isitap) iFound = FindRecord(atm,res,rnum,chn,SIZEFILE,radu);
radu = radu*fScale;
}
if (isitsf)
{
iresnum = atoi(rnum.c_str());
atmsf[nnatom-1] = false;
if (residsf[iresnum-1]) atmsf[nnatom-1] = true;
}
if(isitap && fZero < abs(chrgv))
{
real rads = min(radu,fPotentialUpperBond*fScale);
SGrid<real> xt;
xt = xn; xt.nX += rads;
vphi = interpl(iGrid,phimap,xt);
aphi = vphi;
xt = xn; xt.nX -= rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nY += rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nY -= rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nZ += rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nZ -= rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
aphi = aphi/6.0;
}
if (isitp || isiti || (isitap && fZero > abs(chrgv)))
{
vphi = interpl(iGrid,phimap,xn);
if (isitap && fZero > abs(chrgv)) aphi = vphi;
if (isitp) { etot += chrgv*vphi; phiv = vphi; }
if (isiti)
{
CNoIDebMap warning;
/*
* we have changed the iconc action so that the phimap has NOT been converted to salt concentrations. therefore
*/
if (0 != iNonIterateNum)
{
temp = vphi*fTaylorCoeff5+fTaylorCoeff4; temp = vphi*temp+fTaylorCoeff3;
temp = vphi*temp+fTaylorCoeff2; temp = vphi*temp+fTaylorCoeff1;
phii = vphi*temp;
}
else
phii = -fIonStrength*2.0*vphi;
}
} //----- end if isitp or isiti, salt and or potentials
if (isitdeb) // it calculates the fraction of closest grid points that are in solution
{
cout << "Calculating Debye Fraction\n";
debyefraction = boolinterpl(iGrid,prgbDielecMap,xn);
}
if (isitf)
{
xn.nX += 1.0; fu.nX = interpl(iGrid,phimap,xn);
xn.nX -= 2.0; fl.nX = interpl(iGrid,phimap,xn);
xn.nX += 1.0; xn.nY += 1.0; fu.nY = interpl(iGrid,phimap,xn);
xn.nY -= 2.0; fl.nY = interpl(iGrid,phimap,xn);
xn.nY += 1.0; xn.nZ += 1.0; fu.nZ = interpl(iGrid,phimap,xn);
xn.nZ -= 2.0; fl.nZ = interpl(iGrid,phimap,xn);
xn.nZ += 1.0;
fxyz = (fl-fu)*0.5*fScale; // the electric field is opposite the potential gradient so I change the sign
}
/*
* check if this point is within the box.
*/
if (isitt)
{
SExtrema<real> bedge;
bedge.nMin = fgBoxCenter-0.5*(iGrid-1)/fScale; bedge.nMax = fgBoxCenter+0.5*(iGrid-1)/fScale;
int it = 0;
if ( optORLT<real>(xo,bedge.nMin) || optORGT<real>(xo,bedge.nMax) ) it = 1;
if (0 == it)
{
xo2 = (xo-fgBoxCenter)*fScale+goff;
/*
* first find reaction field from surface elements inside of the box..
*/
phir=0.0; phias=0.0; ncrgs=0; tcrgs=0.0; sold.assign(30,0.0);
for (integer i = 0; i < iDielecBndySum; i++)
{
vtemp = xo - prgfgSurfCrgA[i]; dist = sqrt(optDot(vtemp,vtemp));
//----- first find reaction field from surface elements inside of the box
ncrgs++; tcrgs += prgfSurfCrgE[i]; phirtt = prgfSurfCrgE[i]/dist;
//----- medeps either epsin contain the 561.0 factor....
phirtt = phirtt*fEPKT; phir += phirtt;
xu2.nX = (real)prgigBndyGrid[i].nX; xu2.nY = (real)prgigBndyGrid[i].nY; xu2.nZ = (real)prgigBndyGrid[i].nZ;
crgs = prgfSurfCrgE[i];
//----- took place of repsin because eps is no more included in schrg , surface charge
phiat = tops(xu2,xo2,crgs,1.0,1); phiat = phiat*2.0; phias += phiat;
idist = (int)dist; sold[idist] += phiat - phirtt;
}
temp = 0.0;
cout << "Writing sold(1:30) and temp \n";
for (integer i = 0; i < 30; i++)
{
temp += sold[i];
cout << sold[i] << " " << temp;
}
cout << endl;
/*
* next find the colombic potential for that site from charges within the box
*/
phic = 0.0; phiac = 0.0; ncrg = 0;
for (integer i = 0; i < iCrgGridNum; i++)
{
it = 0;
if (optORLT<real>(prgfgCrgPoseA[i],bedge.nMin) || optORGT<real>(prgfgCrgPoseA[i],bedge.nMax)) it = 1;
if (0 == it)
{
ncrg++;
vtemp = xo - prgfgCrgPoseA[i]; dist = sqrt(optDot(vtemp,vtemp));
if (5.0 > dist)
{
if (fZero < dist) {temp = prggvAtomicCrg[i].nValue/dist; phic += temp/prgfAtomEps[i];}
//----- find analytic potential from this real charge..=phiac
xu = prgfgCrgPoseA[i]; crgs = prggvAtomicCrg[i].nValue;
xu2 = (xu-fgBoxCenter)*fScale+goff;
eps = prgfAtomEps[i]*fEPKT;
phiact = tops(xu2,xo2,crgs,eps,1);
phiac += phiact;
}
}
}
/*
* medeps, either epsin contain the 561.0 factor....
*/
phiac = phiac*2.0;
/*
* find the grid potentials..
*/
phiv = interpl(iGrid,phimap,xn);
string strFileName7 = "extra.dat";
ofstream ofFileSteam7;
ofFileSteam7.open(strFileName7.c_str());
ofFileSteam7 << phic << " " << phir << " " << phiv << " " << phias << " " << phiac << " "<< ncrg << " "
<< ncrgs << " " << tcrgs << endl;
ofFileSteam7.close();
phit = phic + phir + phiv - phias - phiac;
}
else
phit = 0.0;
/*
* phit contains the total corrected potential
*/
}
if (isitr)
{
scomp.assign(30,0.0); sold.assign(30,0.0); phir = 0.0;
for (integer i = 0; i < iDielecBndySum; i++)
{
vtemp = xo - prgfgSurfCrgA[i]; dist = sqrt(optDot(vtemp,vtemp));
idist = (int)dist;
if (30 > idist) sold[idist] += fEPKT*prgfSurfCrgE[i]/dist;
phir += prgfSurfCrgE[i]/dist;
}
/*
* medeps either epsin contains the 561.0 factor....
*/
phir = phir*fEPKT;
for (integer i = 0; i < 30; i++)
{
if (0 == i) scomp[i] = sold[i];
if (0 != i) scomp[i] = scomp[i-1]+sold[i];
}
phirt += phir*chrgv;
}
/*
* medeps either epsin contains the 561.0 factor....
*/
if (isitrf || isitmd || isittf) rxyz = rfield[nnatom-1]*fEPKT;
if(isitcf || isitmd || isittf)
{
cxyz.nX = 0.0; cxyz.nY = 0.0; cxyz.nZ = 0.0;
if (fZero < abs(chrgv))
{
for (integer i = 0; i < iCrgGridNum; i++)
{
vtemp = xo - prgfgCrgPoseA[i]; dist = optDot(vtemp,vtemp);
if (fZero < dist)
{
sdist = sqrt(dist)*dist;
temp = prggvAtomicCrg[i].nValue/(prgfAtomEps[i]*sdist);
cxyz = cxyz + vtemp*temp;
}
}
/*
* atmeps and medeps and epsin contain the 561.0 factor....
*/
cxyz = cxyz*chrgv;
}
}
if (isitc)
{
phic = 0.0;
for (integer i = 0; i < iCrgGridNum; i++)
{
vtemp = xo - prgfgCrgPoseA[i]; dist = optDot(vtemp,vtemp);
if (fZero < dist)
{
sdist = sqrt(dist);
temp = prggvAtomicCrg[i].nValue/sdist;
phic += temp/prgfAtomEps[i];
}
}
/*
* atmeps and medeps and epsin contain the 561.0 factor....
*/
phict += phic*chrgv;
}
//---------------------------------------------------------------------------------------//
/*
* write out calculated/assigned charges
*
* need otemp cos can not write into a substring apparently
* otemp needs to be at least 15 long to avoid an error!!
*/
oline.assign(80,' '); // reset oline
j = 0;
if (isita)
{
oline.replace(j,16,atdes.substr(0,16));
j += 20;
}
if (isitx)
{
sprintf(otemp,"%10.4f",xo.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",xo.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",xo.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitq)
{
sprintf(otemp,"%10.4f",chrgv); oline.replace(j,10,otemp); j += 10;
}
if (isitp)
{
sprintf(otemp,"%10.4f",phiv); oline.replace(j,10,otemp); j += 10;
#ifdef MCCE
mcce_phiv.push_back(phiv);
#endif
}
if (isiti)
{
sprintf(otemp,"%10.4f",phii); oline.replace(j,10,otemp); j += 10;
}
if (isitr)
{
sprintf(otemp,"%10.4f",phir); oline.replace(j,10,otemp); j += 10;
}
if (isitc)
{
sprintf(otemp,"%10.4f",phic); oline.replace(j,10,otemp); j += 10;
}
if (isitap)
{
sprintf(otemp,"%10.4f",aphi); oline.replace(j,10,otemp); j += 10;
}
if (isitdeb)
{
sprintf(otemp,"%10.4f",debyefraction); oline.replace(j,10,otemp); j += 10;
}
if (isitf)
{
sprintf(otemp,"%10.4f",fxyz.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",fxyz.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",fxyz.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitrf)
{
sprintf(otemp,"%10.4f",rxyz.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",rxyz.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",rxyz.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitcf)
{
sprintf(otemp,"%10.4f",cxyz.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",cxyz.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",cxyz.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isittf)
{
vtemp = rxyz + cxyz;
sprintf(otemp,"%10.4f",vtemp.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",vtemp.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",vtemp.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitmd)
{
vtemp = rxyz + cxyz;
cout << "atom: " << nnatom << " rx= " << rxyz.nX << " cx= " << cxyz.nX << " tx= " << vtemp.nX << endl;
cout << "atom: " << nnatom << " ry= " << rxyz.nY << " cy= " << cxyz.nY << " ty= " << vtemp.nY << endl;
cout << "atom: " << nnatom << " rz= " << rxyz.nZ << " cz= " << cxyz.nZ << " tz= " << vtemp.nZ << endl;
}
if (isitt)
{
sprintf(otemp,"%10.4f",phit); oline.replace(j,10,otemp); j += 10;
}
if (ofrm && isitmp1) ofFileStream << oline << endl;
if (!ofrm && isitmp1)
{
if (isita) ofFileStream << atdes << endl;
if (isitx) ofFileStream << xo << endl;
if (isitq) ofFileStream << chrgv << endl;
if (isitp) ofFileStream << phiv << endl;
if (isiti) ofFileStream << phii << endl;
if (isitr) ofFileStream << phir << endl;
if (isitc) ofFileStream << phic << endl;
if (isitap) ofFileStream << aphi << endl;
if (isitf) ofFileStream << fxyz << endl;
if (isitrf) ofFileStream << rxyz << endl;
if (isitcf) ofFileStream << cxyz << endl;
if (isittf) { vtemp = rxyz + cxyz; ofFileStream << vtemp << endl;}
}
} while(true); // end of the big loop on natom
}
if (isitsf)
{
for (integer jj = 0; jj < iBndyGridNum; jj++)
{
integer i = prgiAtSurf[jj];
if (atmsf[i-1] && (0 < prgiAtNdx[jj]))
{
/*
* if the bgp belongs to the interesting site
* attention: using always radprb(1), in some case might be inappropriate
*/
xo = prgfgSurfCrgA[jj]+rgfProbeRadius[0]*prgfgSurfCrgE[jj];
xn = (xo-fgBoxCenter)*fScale+goff;
xn.nX += 1.0; fu.nX = interpl(iGrid,phimap,xn);
xn.nX -= 2.0; fu.nX = interpl(iGrid,phimap,xn);
xn.nX += 1.0; xn.nY += 1.0; fu.nY = interpl(iGrid,phimap,xn);
xn.nY -= 2.0; fu.nY = interpl(iGrid,phimap,xn);
xn.nY += 1.0; xn.nZ += 1.0; fu.nZ = interpl(iGrid,phimap,xn);
xn.nZ -= 2.0; fu.nZ = interpl(iGrid,phimap,xn);
xn.nZ += 1.0;
fxyz = fl - fu;
fn = 0.5*fScale*(optDot(fxyz,prgfgSurfCrgE[jj]));
ff = 0.5*fScale*(optDot(fxyz,fxyz));
if (ofrm)
{
jtmp = j;
sprintf(otemp,"%10.4f",prgfSurfCrgE[jj]); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",xo.nX); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",xo.nY); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",xo.nZ); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",fn); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",ff); oline.replace(jtmp,10,otemp); jtmp += 10;
ofFileStream << oline << endl;
}
if (!ofrm) ofFileStream << prgfSurfCrgE[jj] << " " << fn << endl;
}
}
}
if(!iself) ifFileStream.close();
#ifdef VERBOSE
cout << "\n number of atom coordinates read : " << nnatom << endl << endl;
#endif
etot = etot/2.0;
if (ofrm)
{
if (0 == iFrcFormatOut)
{
ofFileStream << "total energy = " << etot << " kt\n";
if (isitr) ofFileStream << "corrected reaction field energy= " << phirt/2.0 << " kt\n";
if (isitap) ofFileStream << "Atomic potential for charged atoms is averaged over a spherical surface of less than "
<< fPotentialUpperBond << " A\n";
}
if (1 == iFrcFormatOut)
{
ofFileStream << "corrected reaction field energy= " << phirt/2.0 << " kt\n";
ofFileStream << "total coulombic energy = " << phict/2.0 << " kt\n";
if (isitap) ofFileStream << "Atomic potential for charged atoms is averaged over a spherical surface of less than "
<< fPotentialUpperBond << " A\n";
}
if (2 == iFrcFormatOut)
{
ofFileStream << "corrected reaction field energy= " << phirt/2.0 << " kt\n";
if (isitap) ofFileStream << "Atomic potential for charged atoms is averaged over a spherical surface of less than "
<< fPotentialUpperBond << " A\n";
}
}
/*
* end of formatted frc read/write and unformatted frc write
* end of unformatted frc.pdb read and frc write
*/
if (ofFileStream.is_open()) ofFileStream.close();
#ifdef VERBOSE
cout << "frc stuff now done at "; pTimer->showTime(); cout << endl;
#endif
}
int main(void) {
char in[BUFF_SIZE], out[BUFF_SIZE];
register ssize_t wsz = 0, rsz, trsz; /* written bytes, read bytes and total processed bytes */
for (;;) {
trsz = 0;
while ((INPUT - trsz) && (rsz = read(0, in + trsz, INPUT - trsz)) > 0) trsz += rsz;
/*printf("%ld chars read\n", rsz);*/
register char* f = in;
register pile* prev = 0;
register pile* p;
register pile* last;
p = deck;
for (p = deck;; ++p) {
/*
c = fgetc(stdin);
v = fgetc(stdin);
*/
c = *f++;
if (c == '#') goto end;
v = *f++;
/*
fgetc(stdin);
*/
f++;
reset(&p->cards);
push(&p->cards, c, v);
p->prev = prev;
if (prev) prev->next = p;
prev = p;
if (p == &deck[51]) break;
}
p->next = 0;
p = deck;
last = 0;
while (p) {
pile* m = 0;
pile* p3 = p;
if ((p3 = p->prev) && (p3 = p3->prev) && (p3 = p3->prev)) {
if (topv(&p3->cards) == topv(&p->cards) || tops(&p3->cards) == tops(&p->cards)) {
m = p3;
}
}
pile* p1 = 0;
if (!m && (p1 = p->prev)) {
if (topv(&p1->cards) == topv(&p->cards) || tops(&p1->cards) == tops(&p->cards)) {
m = p1;
}
}
if (m) {
push(&m->cards, topv(&p->cards), tops(&p->cards));
pop(&p->cards);
if (!size(&p->cards)) {
p->prev->next = p->next;
if (p->next) p->next->prev = p->prev;
}
p = m;
} else {
last = p;
p = p->next;
}
}
int sz = 1;
p = last;
while (p->prev) {
++sz;
p = p->prev;
}
if (sz > 9)
out[wsz++] = sz / 10 + '0';
out[wsz++] = sz % 10 + '0';
out[wsz++] = ' ';
register const char* of;
if (sz == 1)
of = str_p1;
else
of = str_p2;
while (*of) out[wsz++] = *of++;
out[wsz++] = ' ';
of = str_r;
while (*of) out[wsz++] = *of++;
/*
* above is equal to this
printf("%d %s %s", sz, (sz == 1) ? str_p1 : str_p2, str_r);
*/
while (p) {
sz = size(&p->cards);
out[wsz++] = ' ';
if (sz > 9)
out[wsz++] = sz / 10 + '0';
out[wsz++] = sz % 10 + '0';
p = p->next;
}
out[wsz++] = '\n';
/*
* above is equal to this
while (p) {
printf(" %d", size(&p->cards));
p = p->next;
}
printf("\n");
*/
}
end:
trsz = 0;
while ((trsz = write(1, out, wsz - trsz)) > 0);
return 0;
}