/*!
Decrypts cleartext data using EAX' mode (see ANSI Standard C12.22-2008).
@param[in] pN pointer to cleartext (canonified form)
@param[in] pK pointer to secret key
@param[in,out] pC pointer to ciphertext
@param[in] SizeN byte length of cleartext (pN) buffer
@param[in] SizeK byte length of secret key (pK)
@param[in] SizeC byte length of ciphertext (pC) buffer
@param[in] pMac four-byte Message Authentication Code
@param[in] Mode EAX_MODE_CLEARTEXT_AUTH or EAX_MODE_CIPHERTEXT_AUTH
@return TRUE if message has been authenticated; FALSE if not
authenticated, invalid Mode or error
*/
gboolean Eax_Decrypt(guint8 *pN, guint8 *pK, guint8 *pC,
guint32 SizeN, guint32 SizeK, guint32 SizeC, MAC_T *pMac,
guint8 Mode)
{
guint8 wsn[EAX_SIZEOF_KEY];
guint8 wsc[EAX_SIZEOF_KEY];
int i;
/* key size must match this implementation */
if (SizeK != EAX_SIZEOF_KEY)
return FALSE;
/* the key is new */
for (i = 0; i < EAX_SIZEOF_KEY; i++)
instance.L[i] = 0;
AesEncrypt(instance.L, pK);
Dbl(instance.D, instance.L);
Dbl(instance.Q, instance.D);
/* the key is set up */
/* first copy the nonce into our working space */
BLK_CPY(wsn, instance.D);
if (Mode == EAX_MODE_CLEARTEXT_AUTH) {
dCMAC(pK, wsn, pN, SizeN, pC, SizeC);
} else {
CMAC(pK, wsn, pN, SizeN);
}
/*
* In authentication mode the inputs are: pN, pK (and associated sizes),
* the result is the 4 byte MAC.
*/
if (Mode == EAX_MODE_CLEARTEXT_AUTH)
{
return (memcmp(pMac, &wsn[EAX_SIZEOF_KEY-sizeof(*pMac)], sizeof(*pMac)) ? FALSE : TRUE);
}
/*
* In cipher mode the inputs are: pN, pK, pP (and associated sizes),
* the results are pC (and its size) along with the 4 byte MAC.
*/
else if (Mode == EAX_MODE_CIPHERTEXT_AUTH)
{
if (SizeC == 0)
return (memcmp(pMac, &wsn[EAX_SIZEOF_KEY-sizeof(*pMac)], sizeof(*pMac)) ? FALSE : TRUE);
{
/* first copy the nonce into our working space */
BLK_CPY(wsc, instance.Q);
CMAC(pK, wsc, pC, SizeC);
BLK_XOR(wsc, wsn);
}
if (memcmp(pMac, &wsc[EAX_SIZEOF_KEY-sizeof(*pMac)], sizeof(*pMac)) == 0)
{
CTR(wsn, pK, pC, SizeC);
return TRUE;
}
}
return FALSE;
}
/*
* Output histogram
*/
void Distribution::output(std::ostream& out)
{
double x, rho;
for (int i=0; i < nBin_; ++i) {
x = min_ + binWidth_*(double(i) + 0.5);
rho = double(histogram_[i])/double(nSample_);
rho = rho/binWidth_;
out << Dbl(x, 18, 8) << Dbl(rho, 18, 8) << std::endl;
}
}
int
p_sincos(value val_arg, type tag_arg,
value val_sin, type tag_sin,
value val_cos, type tag_cos)
{
extern void sincos(); /* from the math library */
double s, c;
Prepare_Requests;
Error_If_Ref(tag_arg);
Check_Output_Float(tag_sin);
Check_Output_Float(tag_cos);
if (IsDouble(tag_arg))
sincos(Dbl(val_arg), &s, &c);
else if (IsInteger(tag_arg))
sincos((double) val_arg.nint, &s, &c);
else
{
Error(TYPE_ERROR);
}
Request_Unify_Float(val_sin, tag_sin, s);
Request_Unify_Float(val_cos, tag_cos, c);
Return_Unify;
}
/*
* Add a sampled value to the ensemble (private method)
*
* If outFilePtr != 0, output block averages to outFilePtr
*/
void Average::sample(double value, std::ostream* outFilePtr)
{
AverageStage::sample(value);
// Process block average for output
if (nSamplePerBlock_ && outFilePtr) {
blockSum_ += value;
++iBlock_;
if (iBlock_ == nSamplePerBlock_) {
*outFilePtr << Dbl(blockSum_/double(nSamplePerBlock_))
<< std::endl;
blockSum_ = 0.0;
iBlock_ = 0;
}
}
}
/*
* Output results to file after simulation is completed.
*/
void ClusterHistogram::output()
{
// Write parameter file
fileMaster().openOutputFile(outputFileName(".prm"), outputFile_);
writeParam(outputFile_);
outputFile_.close();
// Write histogram output
fileMaster().openOutputFile(outputFileName(".hist"), outputFile_);
// hist_.output(outputFile_);
int min = hist_.min();
int nBin = hist_.nBin();
for (int i = 0; i < nBin; ++i) {
outputFile_ << Int(i + min) << " "
<< Dbl(double(hist_.data()[i])/double(nSample_)) << "\n";
}
outputFile_.close();
}
ppw(pword *pw) /* print prolog words */
{
int arity = 1;
pword *queue_head = (pword *) 0;
pword *queue_tail = (pword *) 0;
for (;;)
{
char region;
int t = TagType(pw->tag);
if (t < TFORWARD || t > TBUFFER)
t = TUNKNOWN;
if (TG_ORIG <= pw && pw < TG) region = 'g';
else if (SP <= pw && pw < SP_ORIG) region = 'l';
else if (B_ORIG <= pw && pw < B.args) region = 'c';
else if (TT <= (pword **) pw && (pword **) pw < TT_ORIG) region = 't';
else if (address_in_heap(&global_heap, (generic_ptr) pw)) region = 'h';
else region = '?';
p_fprintf(current_output_, "%c 0x%08x: 0x%08x 0x%08x %s ", region,
pw, pw->val.all, pw->tag.all, tag_string[t-TUNKNOWN]);
switch (t)
{
case TFORWARD:
case TMETA:
case TNAME:
if (pw != pw->val.ptr)
{
ec_outfs(current_output_, "--->");
EnQueue_(pw->val.ptr, 1);
}
else
{
ec_outfs(current_output_, IsNamed(pw->tag.kernel) ?
DidName(TagDid(pw->tag.kernel)) : "_");
}
break;
case TVAR_TAG:
if (pw != pw->val.ptr)
{
ec_outfs(current_output_, "--->");
EnQueue_(pw->val.ptr, 1);
}
else
ec_outfs(current_output_, "_");
break;
case TLIST:
EnQueue_(pw->val.ptr, 2);
break;
case TCOMP:
if (pw->val.ptr)
EnQueue_(pw->val.ptr, DidArity(pw->val.ptr->val.did)+1);
break;
case TSTRG:
ec_outfs(current_output_, StringStart(pw->val));
break;
case TSUSP:
break;
case TDE:
break;
case THANDLE:
break;
case TNIL:
break;
case TINT:
p_fprintf(current_output_, "%d", pw->val.nint);
break;
case TDICT:
ec_outfs(current_output_, DidName(pw->val.did));
if (DidArity(pw->val.did))
p_fprintf(current_output_, "/%d", DidArity(pw->val.did));
break;
case TPTR:
break;
case TPROC:
case TEND:
case TVARNUM:
case TGRS:
case TGRL:
case TEXTERN:
case TBUFFER:
break;
case TDBL:
p_fprintf(current_output_, "%f", Dbl(pw->val));
break;
case TBIG:
case TRAT:
default:
if (t >= 0 && t <= NTYPES)
{
(void) tag_desc[t].write(QUOTED, current_output_,
pw->val, pw->tag);
}
break;
}
ec_newline(current_output_);
if (--arity > 0)
{
pw++;
continue;
}
ec_newline(current_output_);
if (EmptyQueue())
break;
DeQueue_(pw, arity);
}
Succeed_;
}
/*
* Output statistical properties to file
*/
void Average::output(std::ostream& out)
{
// Find first stage (descending) with nSample >= 16
AverageStage* ptr = 0;
int n = descendants_.size();
int i = n;
int nSample = 1;
while (nSample < 16 && i > 0) {
--i;
ptr = descendants_[i];
nSample = ptr->nSample();
}
double error = ptr->error();
double sigma = error/sqrt(2.0*double(nSample-1));
double weight = 1.0/(sigma*sigma);
double sum = error*weight;
double norm = weight;
double aveErr = error;
double oldSig;
// Find weighted average within plateau
bool next = true;
while (next && i > 0) {
oldSig = sigma;
--i;
ptr = descendants_[i];
error = ptr->error();
if (fabs(error - aveErr) < 2.0*oldSig) {
nSample = ptr->nSample();
sigma = error/sqrt(2.0*double(nSample-1));
weight = 1.0/(sigma*sigma);
sum += error*weight;
norm += weight;
aveErr = sum/norm;
} else {
next = false;
}
}
out << "Average " << Dbl(average())
<< " +- " << Dbl(aveErr, 9, 2) << std::endl;
out << "Variance " << Dbl(variance()) << std::endl;
out << "Std Dev " << Dbl(stdDeviation()) << std::endl;
out << std::endl;
out << "Hierarchichal Error Analysis:" << std::endl;
int interval;
for (int i = 0; i < n; ++i) {
ptr = descendants_[i];
error = ptr->error();
nSample = ptr->nSample();
interval = ptr->stageInterval();
if (nSample >= 16) {
out << Int(i)
<< Int(interval)
<< Dbl(error)
<< Dbl(error/sqrt(double(nSample)))
<< Int(nSample) << std::endl;
}
}
out << std::endl;
}
/*
* Output statistics.
*/
void Integrator::outputStatistics(std::ostream& out)
{
if (!domain().isMaster()) {
UTIL_THROW("May be called only on domain master");
}
double time = timer().time();
int nAtomTot = atomStorage().nAtomTotal();
int nProc = 1;
#ifdef UTIL_MPI
nProc = domain().communicator().Get_size();
#endif
// Output total time for the run
out << std::endl;
out << "Time Statistics" << std::endl;
out << "nStep " << iStep_ << std::endl;
out << "run time " << time << " sec" << std::endl;
out << "time / nStep " << time/double(iStep_)
<< " sec" << std::endl;
double factor1 = 1.0/double(iStep_);
double factor2 = double(nProc)/(double(iStep_)*double(nAtomTot));
double totalT = 0.0;
out << std::endl;
out << "T = Time per processor, M = nstep = # steps" << std::endl
<< "P = # procs, N = # atoms (total, all processors)"
<< std::endl << std::endl;
out << " "
<< " T/M [sec] "
<< " T*P/(N*M) "
<< " Percent (%)" << std::endl;
out << "Total "
<< Dbl(time*factor1, 12, 6)
<< " "
<< Dbl(time*factor2, 12, 6)
<< " " << Dbl(100.0, 12, 6, true) << std::endl;
double integrate1T = timer().time(INTEGRATE1);
totalT += integrate1T;
out << "Integrate1 "
<< Dbl(integrate1T*factor1, 12, 6)
<< " "
<< Dbl(integrate1T*factor2, 12, 6)
<< " " << Dbl(100.0*integrate1T/time, 12, 6, true) << std::endl;
double checkT = timer().time(CHECK);
totalT += checkT;
out << "Check "
<< Dbl(checkT*factor1, 12, 6)
<< " "
<< Dbl(checkT*factor2, 12, 6)
<< " " << Dbl(100.0*checkT/time, 12, 6, true) << std::endl;
double allReduceT = timer().time(ALLREDUCE);
totalT += allReduceT;
out << "AllReduce "
<< Dbl(allReduceT*factor1, 12, 6)
<< " "
<< Dbl(allReduceT*factor2, 12, 6)
<< " " << Dbl(100.0*allReduceT/time, 12, 6, true) << std::endl;
double transformFT = timer().time(TRANSFORM_F);
totalT += transformFT;
out << "Transform (forward) "
<< Dbl(transformFT*factor1, 12, 6)
<< " "
<< Dbl(transformFT*factor2, 12, 6)
<< " " << Dbl(100.0*transformFT/time, 12, 6, true) << std::endl;
double exchangeT = timer().time(EXCHANGE);
totalT += exchangeT;
out << "Exchange "
<< Dbl(exchangeT*factor1, 12, 6)
<< " "
<< Dbl(exchangeT*factor2, 12, 6)
<< " " << Dbl(100.0*exchangeT/time, 12, 6, true) << std::endl;
double cellListT = timer().time(CELLLIST);
totalT += cellListT;
out << "CellList "
<< Dbl(cellListT*factor1, 12, 6)
<< " "
<< Dbl(cellListT*factor2, 12, 6)
<< " " << Dbl(100.0*cellListT/time, 12, 6, true) << std::endl;
double transformRT = timer().time(TRANSFORM_R);
totalT += transformRT;
out << "Transform (reverse) "
<< Dbl(transformRT*factor1, 12, 6)
<< " "
<< Dbl(transformRT*factor2, 12, 6)
<< " " << Dbl(100.0*transformRT/time, 12, 6, true) << std::endl;
double pairListT = timer().time(PAIRLIST);
totalT += pairListT;
out << "PairList "
<< Dbl(pairListT*factor1, 12, 6)
<< " "
<< Dbl(pairListT*factor2, 12, 6)
<< " " << Dbl(100.0*pairListT/time, 12, 6, true) << std::endl;
double updateT = timer().time(UPDATE);
totalT += updateT;
out << "Update "
<< Dbl(updateT*factor1, 12, 6)
<< " "
<< Dbl(updateT*factor2, 12, 6)
<< " " << Dbl(100.0*updateT/time, 12, 6, true) << std::endl;
double zeroForceT = timer().time(ZERO_FORCE);
totalT += zeroForceT;
out << "Zero Forces "
<< Dbl(zeroForceT*factor1, 12, 6)
<< " "
<< Dbl(zeroForceT*factor2, 12, 6)
<< " " << Dbl(100.0*zeroForceT/time, 12 , 6, true) << std::endl;
double pairForceT = timer().time(PAIR_FORCE);
totalT += pairForceT;
out << "Pair Forces "
<< Dbl(pairForceT*factor1, 12, 6)
<< " "
<< Dbl(pairForceT*factor2, 12, 6)
<< " " << Dbl(100.0*pairForceT/time, 12 , 6, true) << std::endl;
#ifdef INTER_BOND
if (nBondType()) {
double bondForceT = timer().time(BOND_FORCE);
totalT += bondForceT;
out << "Bond Forces "
<< Dbl(bondForceT*factor1, 12, 6)
<< " "
<< Dbl(bondForceT*factor2, 12, 6)
<< " " << Dbl(100.0*bondForceT/time, 12 , 6, true) << std::endl;
}
#endif
#ifdef INTER_ANGLE
if (nAngleType()) {
double angleForceT = timer().time(ANGLE_FORCE);
totalT += angleForceT;
out << "Angle Forces "
<< Dbl(angleForceT*factor1, 12, 6)
<< " "
<< Dbl(angleForceT*factor2, 12, 6)
<< " " << Dbl(100.0*angleForceT/time, 12 , 6, true) << std::endl;
}
#endif
#ifdef INTER_DIHEDRAL
if (nDihedralType()) {
double dihedralForceT = timer().time(DIHEDRAL_FORCE);
totalT += dihedralForceT;
out << "Dihedral Forces "
<< Dbl(dihedralForceT*factor1, 12, 6)
<< " "
<< Dbl(dihedralForceT*factor2, 12, 6)
<< " " << Dbl(100.0*dihedralForceT/time, 12 , 6, true) << std::endl;
}
#endif
#ifdef INTER_EXTERNAL
if (hasExternal()) {
double externalForceT = timer().time(DIHEDRAL_FORCE);
totalT += externalForceT;
out << "External Forces "
<< Dbl(externalForceT*factor1, 12, 6)
<< " "
<< Dbl(externalForceT*factor2, 12, 6)
<< " " << Dbl(100.0*externalForceT/time, 12 , 6, true) << std::endl;
}
#endif
double integrate2T = timer().time(INTEGRATE2);
totalT += integrate2T;
out << "Integrate2 "
<< Dbl(integrate2T*factor1, 12, 6)
<< " "
<< Dbl(integrate2T*factor2, 12, 6)
<< " " << Dbl(100.0*integrate2T/time, 12, 6, true) << std::endl;
double analyzerT = timer().time(ANALYZER);
totalT += analyzerT;
out << "Analyzers "
<< Dbl(analyzerT*factor1, 12, 6)
<< " "
<< Dbl(analyzerT*factor2, 12, 6)
<< " " << Dbl(100.0*analyzerT/time, 12, 6, true) << std::endl;
#ifdef DDMD_MODIFIERS
double modifierT = timer().time(MODIFIER);
totalT += modifierT;
out << "Modifiers "
<< Dbl(modifierT*factor1, 12, 6)
<< " "
<< Dbl(modifierT*factor2, 12, 6)
<< " " << Dbl(100.0*modifierT/time, 12, 6, true) << std::endl;
#endif
out << std::endl;
// Output info about timer resolution
double tick = MPI::Wtick();
out << "Timer resolution "
<< Dbl(tick, 12, 6)
<< " "
<< Dbl(tick*double(nProc)/double(nAtomTot), 12, 6)
<< " " << Dbl(100.0*tick*double(iStep_)/time, 12, 6, true)
<< std::endl;
out << std::endl;
// Output exchange / reneighbor statistics
int buildCounter = pairPotential().pairList().buildCounter();
out << "buildCounter "
<< Int(buildCounter, 12)
<< std::endl;
out << "steps per build "
<< Dbl(double(iStep_)/double(buildCounter), 12, 6)
<< std::endl;
out << std::endl;
}
pword *
term_to_dbformat(pword *parg, dident mod)
{
pword **save_tt = TT;
register word arity = 1, len;
register word curr_offset = 0, top_offset = 2; /* in 'word's */
register pword *queue_tail = (pword *) 0;
pword *queue_head = (pword *) 0;
register pword *pw;
register char *dest, *stop;
pword *header;
temp_area meta_attr;
int flag = 0;
Temp_Create(meta_attr, 4 * ATTR_IO_TERM_SIZE * sizeof(pword));
header = TG;
dest = (char *) (header + 1) + 4; /* space for the TBUFFER pword and for
* the external format header */
for(;;) /* handle <arity> consecutive pwords, starting at <parg> */
{
do /* handle the pword pointed to by parg */
{
pw = parg;
/* I need here a slightly modified version of Dereference_(pw)
* that stops also at MARKed words. Not very nice, I know.
*/
while (IsRef(pw->tag) && !(pw->tag.kernel & MARK) && !IsSelfRef(pw))
pw = pw->val.ptr;
Reserve_Space(6);
if (pw->tag.kernel & MARK)
{
if (SameTypeC(pw->tag,TDE)) /* a suspension */
{
Store_Byte(Tag(pw->tag.kernel));
Store_Int32((pw[SUSP_FLAGS].tag.kernel & ~MARK));
if (SuspDead(pw)) {
curr_offset += Words(SUSP_HEADER_SIZE-1);
parg += SUSP_HEADER_SIZE-1;
arity -= SUSP_HEADER_SIZE-1;
} else {
Store_Byte(SuspPrio(pw) + (SuspRunPrio(pw) << 4));
curr_offset += Words(SUSP_GOAL-1);
parg += SUSP_GOAL-1;
arity -= SUSP_GOAL-1;
}
}
else if (pw->val.nint == curr_offset) /* a nonstd variable */
{
Store_Byte(Tag(pw->tag.kernel));
Store_Int(pw->val.nint);
if (!IsNamed(pw->tag.kernel))
{
Store_Byte(0);
}
else /* store its name */
{
dident vdid = TagDid(pw->tag.kernel);
len = DidLength(vdid);
Store_Int(len);
Reserve_Space(len);
Store_String(len, DidName(vdid));
}
}
else /* just a reference to an already encountered variable */
{
Store_Byte(Tag(TVAR_TAG));
Store_Int(pw->val.nint);
}
}
else switch (TagType(pw->tag))
{
case TINT:
#if SIZEOF_CHAR_P > 4
if (pw->val.nint < WSUF(-2147483648) || WSUF(2147483648) <= pw->val.nint)
{
/* store as a bignum (to be readable on 32bit machines) */
len = tag_desc[pw->tag.kernel].string_size(pw->val, pw->tag, 1);
Store_Byte(TBIG);
Store_Int(len);
Reserve_Space(len+1);
stop = dest+len;
dest += tag_desc[pw->tag.kernel].to_string(pw->val, pw->tag,
dest, 1);
while (dest <= stop) /* pad and terminate */
*dest++ = 0;
break;
}
#endif
Store_Byte(TINT);
#ifdef OLD_FORMAT
Store_Int32(pw->val.nint);
#else
Store_Int(pw->val.nint);
#endif
break;
case TNIL:
Store_Byte(Tag(pw->tag.kernel));
break;
case TDICT:
len = DidLength(pw->val.did);
Store_Byte(TDICT);
Store_Int(DidArity(pw->val.did));
Store_Int(len);
Reserve_Space(len);
Store_String(len, DidName(pw->val.did));
break;
case TDBL:
{
ieee_double d;
d.as_dbl = Dbl(pw->val);
Store_Byte(TDBL);
Store_Byte(sizeof(double)-1); /* backward compat */
Reserve_Space(sizeof(double));
Store_Int32(d.as_struct.mant1);
Store_Int32(d.as_struct.mant0);
break;
}
case TIVL:
{
ieee_double dlwb, dupb;
dlwb.as_dbl = IvlLwb(pw->val.ptr);
dupb.as_dbl = IvlUpb(pw->val.ptr);
Store_Byte(TIVL);
Reserve_Space(2*sizeof(double));
Store_Int32(dlwb.as_struct.mant1);
Store_Int32(dlwb.as_struct.mant0);
Store_Int32(dupb.as_struct.mant1);
Store_Int32(dupb.as_struct.mant0);
break;
}
case TSTRG:
len = StringLength(pw->val);
Store_Byte(TSTRG);
Store_Int(len);
Reserve_Space(len);
Store_String(len, StringStart(pw->val));
break;
case TVAR_TAG: /* standard variable */
Store_Byte(Tag(TVAR_TAG));
Store_Int(curr_offset);
Trail_(pw);
pw->val.nint = curr_offset;
pw->tag.kernel |= MARK;
break;
case TNAME:
case TUNIV:
Store_Byte(Tag(TVAR_TAG));
Store_Int(top_offset);
Trail_Tag(pw);
pw->val.nint = top_offset;
pw->tag.kernel |= MARK;
top_offset += 2;
EnQueue_(pw, 1, 0);
break;
case TMETA:
Store_Byte(Tag(TVAR_TAG));
Store_Int(top_offset);
Trail_Tag(pw);
pw->val.nint = top_offset;
pw->tag.kernel |= MARK;
top_offset += 4;
EnQueue_(pw, 2, QUEUE_MASK_META);
break;
case TSUSP:
Store_Byte(Tag(TSUSP));
pw = pw->val.ptr;
if (pw->tag.kernel & MARK) /* not the first encounter */
{
Store_Int(pw->val.nint);
}
else
{
Store_Int(top_offset);
Trail_Pword(pw);
pw->tag.kernel |= MARK;
pw->val.nint = top_offset;
if (SuspDead(pw))
{
top_offset += Words(SUSP_HEADER_SIZE); /* for TDE */
EnQueue_(pw, SUSP_HEADER_SIZE, 0);
}
else
{
top_offset += Words(SUSP_SIZE); /* for TDE */
EnQueue_(pw, SUSP_SIZE, 0);
}
}
break;
case TLIST:
Store_Byte(Tag(TLIST));
Store_Int(top_offset);
top_offset += 4;
EnQueue_(pw->val.ptr, 2, 0);
break;
case TCOMP:
Store_Byte(Tag(TCOMP));
Store_Int(top_offset);
if (flag) {
pword pw_out;
(void) transf_meta_out(pw->val, pw->tag,
(pword *) TempAlloc(meta_attr, ATTR_IO_TERM_SIZE * sizeof(pword)),
D_UNKNOWN, &pw_out);
pw = pw_out.val.ptr;
len = 1 + DidArity(pw->val.did);
EnQueue_(pw, len, 0);
} else {
len = 1 + DidArity(pw->val.ptr->val.did);
EnQueue_(pw->val.ptr, len, 0);
}
top_offset += 2*len;
break;
default:
if (TagType(pw->tag) >= 0 && TagType(pw->tag) <= NTYPES)
{
len = tag_desc[TagType(pw->tag)].string_size(pw->val, pw->tag, 1);
Store_Byte(Tag(pw->tag.kernel));
Store_Int(len);
Reserve_Space(len+1);
stop = dest+len;
dest += tag_desc[TagType(pw->tag)].to_string(pw->val, pw->tag,
dest, 1);
while (dest <= stop) /* pad and terminate */
*dest++ = 0;
}
else
{
p_fprintf(current_err_,
"bad type in term_to_dbformat: 0x%x\n",
pw->tag.kernel);
}
break;
}
curr_offset += Words(1);
++parg;
} while (--arity);
if (EmptyQueue())
break;
DeQueue_(parg, arity, flag);
}
/* # bytes of external representation */
Store_Byte(0); /* add a terminating 0 */
Set_Buffer_Size(header, dest - (char*) header - sizeof(pword));
header->tag.kernel = TBUFFER;
Align(); /* align the global stack pointer */
TG = (pword *) dest;
dest = (char *) (header + 1); /* fill in the external format header */
Store_Int32(top_offset); /* (size of term after restoring) */
Untrail_Variables(save_tt);
Temp_Destroy(meta_attr);
return header;
}
void ChainMaker::writeChainsDdMd(std::ostream& out)
{
Vector r;
Vector velocity;
Vector v;
double beta = 1.0;
int atomType = 0;
int bondType = 0;
int iMol, iAtom, i, j;
out << "BOUNDARY" << std::endl;
out << std::endl;
out << boundary_ << std::endl;
out << std::endl;
out << "ATOMS" << std::endl;
out << "nAtom " << nMolecule_*nAtomPerMolecule_ << std::endl;
i = 0;
velocity.zero();
for (iMol = 0; iMol < nMolecule_; ++iMol) {
boundary_.randomPosition(random_, r);
for (iAtom = 0; iAtom < nAtomPerMolecule_; ++iAtom) {
out << Int(i,6) << Int(atomType, 10);
for (j = 0; j < Dimension; ++j) {
out << Dbl(r[j], 15, 6);
}
out << " ";
for (j = 0; j < Dimension; ++j) {
out << Dbl(0.0, 12, 4);
}
out << std::endl;
if (iAtom < nAtomPerMolecule_ - 1) {
random_.unitVector(v);
v *= bondPotential_.randomBondLength(&random_, beta, bondType);
r += v;
boundary_.shift(r);
}
++i;
}
}
// Write bonds
out << std::endl;
out << "BONDS" << std::endl;
out << "nBond " << nMolecule_*(nAtomPerMolecule_ -1 ) << std::endl;
i = 0;
j = 0;
for (iMol = 0; iMol < nMolecule_; ++iMol) {
for (iAtom = 0; iAtom < nAtomPerMolecule_ - 1; ++iAtom) {
out << Int(j,5) << Int(bondType, 5) << " ";
out << Int(i, 10) << Int(i + 1, 10) << std::endl;
++i;
++j;
}
++i;
}
// Write angles
int angleType = 0;
out << std::endl;
out << "ANGLES" << std::endl;
out << "nAngle " << nMolecule_*(nAtomPerMolecule_ -2) << std::endl;
i = 0;
j = 0;
for (iMol = 0; iMol < nMolecule_; ++iMol) {
for (iAtom = 0; iAtom < nAtomPerMolecule_ - 2; ++iAtom) {
out << Int(j,5) << Int(angleType, 5) << " ";
out << Int(i, 10) << Int(i + 1, 10) << Int(i + 2, 10)
<< std::endl;
++i;
++j;
}
i += 2;
}
// Write dihedrals
int dihedralType = 0;
out << std::endl;
out << "DIHEDRALS" << std::endl;
out << "nDihedral " << nMolecule_*(nAtomPerMolecule_ -3) << std::endl;
i = 0;
j = 0;
for (iMol = 0; iMol < nMolecule_; ++iMol) {
for (iAtom = 0; iAtom < nAtomPerMolecule_ - 3; ++iAtom) {
out << Int(j,5) << Int(dihedralType, 5) << " ";
out << Int(i, 10) << Int(i + 1, 10) << Int(i + 2, 10)
<< Int(i + 3, 10) << std::endl;
++i;
++j;
}
i += 3;
}
}