AVIFileSink::~AVIFileSink() {
completeOutputFile();
// Then, stop streaming and delete each active "AVISubsessionIOState":
MediaSubsessionIterator iter(fInputSession);
MediaSubsession* subsession;
while ((subsession = iter.next()) != NULL) {
if (subsession->readSource() != NULL) subsession->readSource()->stopGettingFrames();
AVISubsessionIOState* ioState
= (AVISubsessionIOState*)(subsession->miscPtr);
if (ioState == NULL) continue;
delete ioState;
}
// Then, delete the index records:
AVIIndexRecord* cur = fIndexRecordsHead;
while (cur != NULL) {
AVIIndexRecord* next = cur->next();
delete cur;
cur = next;
}
// Finally, close our output file:
CloseOutputFile(fOutFid);
}
void HIDCaptureThread::WriteCapturedDataToFile(bool bWriteToFile, QString qsFileName, bool bWriteHeaderInfo, bool bWriteFilteredData)
{
m_bWriteToFile = bWriteToFile;
m_bWriteHeaderInfo = bWriteHeaderInfo;
m_bWriteFilteredData = bWriteFilteredData;
if ((qsFileName != "") && (qsFileName != m_qsFileName))
{
m_qsFileName = qsFileName;
CloseOutputFile();
}
}
void RunOpt (CodeSeg* S)
/* Run the optimizer */
{
const char* StatFileName;
/* If we shouldn't run the optimizer, bail out */
if (!S->Optimize) {
return;
}
/* Check if we are requested to write optimizer statistics */
StatFileName = getenv ("CC65_OPTSTATS");
if (StatFileName) {
ReadOptStats (StatFileName);
}
/* Print the name of the function we are working on */
if (S->Func) {
Print (stdout, 1, "Running optimizer for function `%s'\n", S->Func->Name);
} else {
Print (stdout, 1, "Running optimizer for global code segment\n");
}
/* If requested, open an output file */
OpenDebugFile (S);
WriteDebugOutput (S, 0);
/* Generate register info for all instructions */
CS_GenRegInfo (S);
/* Run groups of optimizations */
RunOptGroup1 (S);
RunOptGroup2 (S);
RunOptGroup3 (S);
RunOptGroup4 (S);
RunOptGroup5 (S);
RunOptGroup6 (S);
RunOptGroup7 (S);
/* Free register info */
CS_FreeRegInfo (S);
/* Close output file if necessary */
if (DebugOptOutput) {
CloseOutputFile ();
}
/* Write statistics */
if (StatFileName) {
WriteOptStats (StatFileName);
}
}
AVIFileSink::~AVIFileSink() {
completeOutputFile();
// Then, delete each active "AVISubsessionIOState":
MediaSubsessionIterator iter(fInputSession);
MediaSubsession* subsession;
while ((subsession = iter.next()) != NULL) {
AVISubsessionIOState* ioState
= (AVISubsessionIOState*)(subsession->miscPtr);
if (ioState == NULL) continue;
delete ioState;
}
// Finally, close our output file:
CloseOutputFile(fOutFid);
}
void MinimalizationSimulation(void)
{
int j,k;
REAL Drift,ReferenceEnergy,ran;
int NumberOfSystemMoves,NumberOfParticleMoves,NumberOfSteps;
int ran_int;
Drift=0.0;
ReferenceEnergy=0.0;
CurrentSystem=0;
fprintf(stderr, "Starting minimization\n");
OpenOutputFile();
//InitializeNoseHooverAllSystems();
InitializesEnergiesAllSystems();
InitializesEnergyAveragesAllSystems();
InitializeSmallMCStatisticsAllSystems();
InitializeMCMovesStatisticsAllSystems();
CalculateTotalEnergyAllSystems();
PrintPreSimulationStatus();
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
for(k=0;k<NumberOfCycles;k++)
{
InitializesEnergiesAllSystems();
InitializesEnergyAveragesAllSystems();
CalculateTotalEnergyAllSystems();
for(CurrentCycle=0;CurrentCycle<NumberOfInitializationCycles;CurrentCycle++)
{
if((CurrentCycle%PrintEvery)==0)
PrintIntervalStatusInit(CurrentCycle,NumberOfInitializationCycles,OutputFilePtr[CurrentSystem]);
NumberOfSystemMoves=12;
NumberOfParticleMoves=MAX2(MinimumInnerCycles,NumberOfAdsorbateMolecules[CurrentSystem]+NumberOfCationMolecules[CurrentSystem]);
NumberOfSteps=(NumberOfSystemMoves+NumberOfParticleMoves)*NumberOfComponents;
for(j=0;j<NumberOfSteps;j++)
{
ran_int=(int)(RandomNumber()*NumberOfSteps);
switch(ran_int)
{
case 0:
if(RandomNumber()<ProbabilityParallelTemperingMove) ParallelTemperingMove();
break;
case 1:
if(RandomNumber()<ProbabilityHyperParallelTemperingMove) HyperParallelTemperingMove();
break;
case 2:
if(RandomNumber()<ProbabilityParallelMolFractionMove) ParallelMolFractionMove();
break;
case 3:
if(RandomNumber()<ProbabilityChiralInversionMove) ChiralInversionMove();
break;
case 4:
if(RandomNumber()<ProbabilityHybridNVEMove) HybridNVEMove();
break;
case 5:
if(RandomNumber()<ProbabilityHybridNPHMove) HybridNPHMove();
break;
case 6:
if(RandomNumber()<ProbabilityHybridNPHPRMove) HybridNPHPRMove();
break;
case 7:
if(RandomNumber()<ProbabilityVolumeChangeMove) VolumeMove();
break;
case 8:
if(RandomNumber()<ProbabilityBoxShapeChangeMove) BoxShapeChangeMove();
break;
case 9:
if(RandomNumber()<ProbabilityGibbsVolumeChangeMove) GibbsVolumeMove();
break;
case 10:
if(RandomNumber()<ProbabilityFrameworkChangeMove) FrameworkChangeMove();
break;
case 11:
if(RandomNumber()<ProbabilityFrameworkShiftMove) FrameworkShiftMove();
break;
default:
// choose component at random
CurrentComponent=(int)(RandomNumber()*(REAL)NumberOfComponents);
// choose the Monte Carlo move at random
ran=RandomNumber();
if(ran<Components[CurrentComponent].ProbabilityTranslationMove)
TranslationMove();
else if(ran<Components[CurrentComponent].ProbabilityRandomTranslationMove)
RandomTranslationMove();
else if(ran<Components[CurrentComponent].ProbabilityRotationMove)
RotationMove();
else if(ran<Components[CurrentComponent].ProbabilityPartialReinsertionMove)
PartialReinsertionMove();
else if(ran<Components[CurrentComponent].ProbabilityReinsertionMove)
ReinsertionMove();
else if(ran<Components[CurrentComponent].ProbabilityReinsertionInPlaceMove)
ReinsertionInPlaceMove();
else if(ran<Components[CurrentComponent].ProbabilityReinsertionInPlaneMove)
ReinsertionInPlaneMove();
else if(ran<Components[CurrentComponent].ProbabilityIdentityChangeMove)
IdentityChangeMove();
else if(ran<Components[CurrentComponent].ProbabilitySwapMove)
{
if(RandomNumber()<0.5) SwapAddMove();
else SwapRemoveMove();
}
else if(ran<Components[CurrentComponent].ProbabilityWidomMove)
;
else if(ran<Components[CurrentComponent].ProbabilitySurfaceAreaMove)
;
else if(ran<Components[CurrentComponent].ProbabilityGibbsChangeMove)
GibbsParticleTransferMove();
else if(ran<Components[CurrentComponent].ProbabilityGibbsIdentityChangeMove)
GibbsIdentityChangeMove();
}
}
if(CurrentCycle%1000==0)
OptimizeTranslationAcceptence();
}
// do the minimization
Minimization(k);
InitializesEnergiesCurrentSystem();
CalculateEnergy();
PrintEnergyStatus(OutputFilePtr[CurrentSystem],"minimization full energy");
}
PrintRestartFile();
}
PrintPostSimulationStatus();
CloseOutputFile();
}
void GlobalMinimumSimulation(void)
{
int i,j,k,l;
int success;
REAL ran,GlobalMinimumEnergy,UInitial,UAfterMC;
success=0;
GlobalMinimumEnergy=EnergyOverlapCriteria;
OpenOutputFile();
PrintPreSimulationStatus();
for(k=0;k<NumberOfCycles;k++)
{
do
{
CurrentSystem=0;
for(i=0;i<NumberOfAdsorbateMolecules[0];i++)
RemoveAdsorbateMolecule();
for(i=0;i<NumberOfCationMolecules[0];i++)
RemoveCationMolecule();
for(j=0;j<NumberOfComponents;j++)
{
if(Components[j].CreateNumberOfMolecules[0]>0)
{
CurrentSystem=0;
if(Components[j].ExtraFrameworkMolecule)
MakeInitialCations(Components[j].CreateNumberOfMolecules[0],j);
else
MakeInitialAdsorbates(Components[j].CreateNumberOfMolecules[0],j);
}
}
CalculateForce();
UInitial=UTotal[0];
for(l=0;l<NumberOfInitializationCycles;l++)
{
for(j=0;j<MAX2(MinimumInnerCycles,NumberOfAdsorbateMolecules[CurrentSystem]+NumberOfCationMolecules[CurrentSystem]);j++)
{
// choose component at random
CurrentComponent=(int)(RandomNumber()*(REAL)NumberOfComponents);
// choose the Monte Carlo move at random
ran=RandomNumber();
if(Components[CurrentComponent].ExtraFrameworkMolecule)
{
if(ran<Components[CurrentComponent].ProbabilityTranslationMove)
TranslationMoveCation();
if(ran<Components[CurrentComponent].ProbabilityRotationMove)
RotationMoveCation();
else if(ran<Components[CurrentComponent].ProbabilityReinsertionMove)
ReinsertionCationMove();
}
else
{
if(ran<Components[CurrentComponent].ProbabilityTranslationMove)
TranslationMoveAdsorbate();
if(ran<Components[CurrentComponent].ProbabilityRotationMove)
RotationMoveAdsorbate();
else if(ran<Components[CurrentComponent].ProbabilityReinsertionMove)
ReinsertionAdsorbateMove();
}
}
}
CalculateForce();
UAfterMC=UTotal[0];
// do the minimization as
//success=BakerMinimizationNoOutput();
if(success==0)
fprintf(OutputFilePtr[0],"Minimization failed to convergence within %d steps\n",MaximumNumberOfMinimizationSteps);
} while(success==0);
// recompute energy
CalculateForce();
CurrentSystem=0;
fprintf(OutputFilePtr[0],"iteration: %d Energy before Monte-Carlo: %18.10f [K] Energy after Monte-Carlo: %18.10f [K]\n",
k,UInitial*ENERGY_TO_KELVIN,UAfterMC*ENERGY_TO_KELVIN);
fflush(OutputFilePtr[0]);
if(UTotal[0]<GlobalMinimumEnergy)
{
fprintf(OutputFilePtr[0],"found lower new minimum, positions saved to restart-file\n");
GlobalMinimumEnergy=UTotal[0];
PrintRestartFile();
}
fprintf(OutputFilePtr[0],"\t\tMinimization steps: %d Minimized energy: %18.10f [K] (%18.10f [kJ/mol]) Global minimum: %18.10f (%18.10f [kJ/mol])\n",
success,UTotal[0]*ENERGY_TO_KELVIN,UTotal[0]*ENERGY_TO_KJ_PER_MOL,GlobalMinimumEnergy*ENERGY_TO_KELVIN,GlobalMinimumEnergy*ENERGY_TO_KJ_PER_MOL);
fflush(OutputFilePtr[0]);
}
PrintPostSimulationStatus();
CloseOutputFile();
}
SRecord2C::~SRecord2C()
{
CloseOutputFile();
}
// ==============================================================
// Extract License & Notes files
// These are stored as 4-bytes length, followed by length-bytes of compressed data
int ExtractTextFile(BLOCK_DATA *Blk, ULONG FileType)
{
ULONG n, m;
BYTE *zSrcBuf = (BYTE *) Blk->SrcBuf;
BYTE *zDstBuf = (BYTE *) Blk->DstBuf;
const char *FileExt;
if (FileType == FLAGS_License)
FileExt = LicenseExt;
else if (FileType == FLAGS_Notes)
FileExt = NotesExt;
else
return 0;
// NB:Can't use BioReadBuf... aligment problems? Yet it works for ProcessNextBlock() !!??
// Ok, can use ReadInputFile here cause everythjing is whole no. of bytes...
//BioReadBuf((BYTE *)&n, sizeof(n)); // Read length of block from file
ReadInputFile((BYTE *)&n, sizeof(n)); // Read length of block from file
FixEndian(&n, sizeof(n)); // Fix endian
if (n <= 0 || n > ZBUF_SIZE) // Check for valid block length
{
sprintf(MsgTxt, "ERROR - Invalid length for %s file (apparently %ld bytes) %s", FileExt, n, CorruptedMsg);
msg(MsgTxt, MSG_PopUp);
GlobalErrorFlag = SFARKLIB_ERR_CORRUPT;
return 0;
}
//BioReadBuf(zSrcBuf, n); // Read the block
ReadInputFile((BYTE *)zSrcBuf, n); // Read the block
m = UnMemcomp(zSrcBuf, n, zDstBuf, ZBUF_SIZE); // Uncompress
Blk->FileCheck = adler32(Blk->FileCheck, zDstBuf, m); // Accumulate checksum
if (GlobalErrorFlag || m > ZBUF_SIZE) // Uncompressed ok & size is valid?
return 0;
// Write file - Use original file name plus specified extension for OutFileName...
char OutFileName[MAX_FILENAME];
strncpy(OutFileName, Blk->FileHeader.FileName, sizeof(OutFileName)); // copy output filename
ChangeFileExt(OutFileName, FileExt, sizeof(OutFileName));
OpenOutputFile(OutFileName); // Create notes / license file
WriteOutputFile(zDstBuf, m); // and write to output file
CloseOutputFile();
if (FileType == FLAGS_License)
{
sprintf(MsgTxt, "Created license file: %s", OutFileName);
msg(MsgTxt, 0);
if (GetLicenseAgreement((const char *)zDstBuf, OutFileName) == 0)
{
GlobalErrorFlag = SFARKLIB_ERR_LICENSE;
return EndProcess(0);
}
}
else if (FileType == FLAGS_Notes)
{
sprintf(MsgTxt, "Created notes file: %s", OutFileName);
msg(MsgTxt, 0);
DisplayNotes((const char *)zDstBuf, OutFileName);
}
return 1;
}
// ==============================================================
int EndProcess(int ErrorNum)
{
CloseInputFile();
CloseOutputFile();
return ErrorNum;
}
HIDCaptureThread::~HIDCaptureThread()
{
stop();
CloseOutputFile();
m_JostickHistory.clear();
}
void HIDCaptureThread::run()
{
bool bAutoGenerateData = false;//For testing purpose
bool bButtonValueChanged = false;
USBHIDDeviceNameSpace::strcJoystickPosition currentJoyPos;
m_bIsRunning = true;
emit receiveThreadStarted(QDateTime::currentDateTime().toString(MainAppInfo::stdDateTimeFormat()));
int res;
unsigned char buf[255];
hid_device *handle;
if(!bAutoGenerateData)
{
memset(buf,0x00,sizeof(buf));
struct hid_device_info *devs, *cur_dev;
devs = hid_enumerate(0x0, 0x0);
cur_dev = devs;
//while (cur_dev) {
// printf("Device Found\n type: %04hx %04hx\n path: %s\n serial_number: %ls", cur_dev->vendor_id, cur_dev->product_id, cur_dev->path, cur_dev->serial_number);
// printf("\n");
// printf(" Manufacturer: %ls\n", cur_dev->manufacturer_string);
// printf(" Product: %ls\n", cur_dev->product_string);
// printf(" Release: %hx\n", cur_dev->release_number);
// printf(" Interface: %d\n", cur_dev->interface_number);
// printf("\n");
// cur_dev = cur_dev->next;
//}
hid_free_enumeration(devs);
// Open the device using the VID, PID, and optionally the Serial number.
handle = hid_open(m_VendorID, m_ProductID, NULL);
if (!handle) {
//printf("unable to open device\n");
emit receiveThreadStopped(QDateTime::currentDateTime().toString(MainAppInfo::stdDateTimeFormat()));
qCritical("HIDCaptureThread: Could not open HID Device");
m_bIsRunning = false;
return;
}
// Set the hid_read() function to be non-blocking.
hid_set_nonblocking(handle, 1);
}
else
{
m_HIDData[0] = 0;
m_HIDData[1] = 0;
m_HIDData[2] = 0;
m_HIDData[3] = 0;
}
while(m_bAbortRunning==false)
{
// Try to read from the device. There should be no
// data here, but execution should not block.
if(!bAutoGenerateData)
{
res = hid_read(handle, buf, sizeof(buf));
}
else
{
res = 4;//We are going to generate these results
}
if (res>1)
{
if(!bAutoGenerateData)
{
//emit captureThreadTriggered();
if(buf[0] > 127)
{
m_HIDData[0] = (buf[0] - 128);
}
else
{
m_HIDData[0] = (buf[0] + 128);
}
if(buf[1] > 127)
{
m_HIDData[1] = (buf[1] - 128);
}
else
{
m_HIDData[1] = (buf[1] + 128);
}
m_HIDData[2] = buf[2];
m_HIDData[3] = buf[3];
//Hereafter the center is at position(x,y) (127|128),(127|128) --> (m_HIDData[0],m_HIDData[1])
//The left point(x) is < 127, right point(x) is > 128 --> m_HIDData[0]
//The top point(y) is < 127, bottom point(y) is > 128 --> m_HIDData[1]
//The Buttons are at m_HIDData[2]; LeftButton = 1, RightButton = 2
//TriggerInput is also at m_HIDData[2], emulates Button;(BNC; inside = TTL, outside = GND) only rising edge(send only a single packet as response)!
}
else//Generate some dummy data for testing
{
m_HIDData[0] = m_HIDData[0]+1;
m_HIDData[1] = m_HIDData[1]+1;
//m_HIDData[2] = m_HIDData[2]+2;
//m_HIDData[3] = m_HIDData[3]+2;
}
if(m_bActivateButtonTriggers)
{
unsigned char cSignalVal;
cNewButtonByteVal = (m_HIDData[2] & m_cButtonMask);
switch (m_ButtonDetectCaptureMethod)
{
case USBHIDDeviceNameSpace::MaskedValueChanged :
if (cOldButtonByteVal != cNewButtonByteVal)//any change within masked measurement
{
emit receiveThreadButtonTriggered(cNewButtonByteVal,cOldButtonByteVal ^ cNewButtonByteVal);//Signal(Difference, Press and Release)
bButtonValueChanged = true;
}
cOldButtonByteVal = cNewButtonByteVal;
break;
case USBHIDDeviceNameSpace::MaskedValueChangedHigh :
cSignalVal = (~cOldButtonByteVal) & cNewButtonByteVal;
if(cSignalVal)//any change from low to high
{
emit receiveThreadButtonTriggered(cNewButtonByteVal,cSignalVal);//Signal(Positive Changes, Press)
bButtonValueChanged = true;
}
cOldButtonByteVal = cNewButtonByteVal;
break;
case USBHIDDeviceNameSpace::MaskedValueChangedLow :
cSignalVal = cOldButtonByteVal & (~cNewButtonByteVal);
if(cSignalVal)//any change from high to low
{
emit receiveThreadButtonTriggered(cNewButtonByteVal,cSignalVal);//Signal(Positive Changes, Release)
bButtonValueChanged = true;
}
cOldButtonByteVal = cNewButtonByteVal;
break;
}
}
//Maintain a history
currentJoyPos.Xpos = m_HIDData[0];
currentJoyPos.Ypos = m_HIDData[1];
while(m_JostickHistory.size() > m_nJoystickHistorySize)
{
m_JostickHistory.pop_front();//Maximum size reached
}
if (m_bActivateJoystickTrigger)//Is the trigger activated?
{
if(m_JostickHistory.size()>0)//Do we already have a history?
{
if(!((m_JostickHistory.last().Xpos == currentJoyPos.Xpos) && (m_JostickHistory.last().Ypos == currentJoyPos.Ypos)))//Only when value changed!
{
if((m_bActivateJoystickStabilisation)&&(m_nJoystickStabilisationThreshold>0))
{
if( ((m_JostickHistory.last().Xpos - m_nJoystickStabilisationThreshold) > currentJoyPos.Xpos) || \
((m_JostickHistory.last().Xpos + m_nJoystickStabilisationThreshold) < currentJoyPos.Xpos) || \
((m_JostickHistory.last().Ypos - m_nJoystickStabilisationThreshold) > currentJoyPos.Ypos) || \
((m_JostickHistory.last().Ypos + m_nJoystickStabilisationThreshold) < currentJoyPos.Ypos) )
//Only when value changed enough!!
{
EmitFilteredData();//Send the trigger
if (!OutputCapturedData()) m_bAbortRunning = true;
}
}
else
{
EmitFilteredData();//Send the trigger
if (!OutputCapturedData()) m_bAbortRunning = true;
}
}
}
else
{
EmitFilteredData();//Send the trigger, first record!
if (!OutputCapturedData()) m_bAbortRunning = true;
}
}
//else if ((m_bActivateButtonTriggers) && (bButtonValueChanged))
//{
//
//}
m_JostickHistory.append(currentJoyPos);//Now add the new data record
}
//QThread::msleep(10);
}
if(!bAutoGenerateData)
hid_close(handle);
CloseOutputFile();
m_bAbortRunning = false;
m_bIsRunning = false;
emit receiveThreadStopped(QDateTime::currentDateTime().toString(MainAppInfo::stdDateTimeFormat()));
return;
}
//使用到numerator、denominator、type、ctrl、起始时间，终止时间
int CSeedManager::CreateOutputFile( const WCHAR* path, CtrlParam* pctrl )
{
int ret = TRUE;
WCHAR filename[MAX_PATH];
//CtrlParam ctrl;
CloseOutputFile();
if(m_list->GetElementCnt() <= 0)
return FALSE;
// memcpy(&ctrl, pctrl, sizeof(CtrlParam));
// wcscpy_s(ctrl.station, sizeof(ctrl.station)/sizeof(WCHAR), m_station);
// wcscpy_s(ctrl.channel, sizeof(ctrl.channel)/sizeof(WCHAR), m_channel);
wcscpy_s(pctrl->station, sizeof(pctrl->station)/sizeof(WCHAR), m_station);
wcscpy_s(pctrl->channel, sizeof(pctrl->channel)/sizeof(WCHAR), m_channel);
if(FALSE == AdjustValidParam(pctrl))
return FALSE;
switch (pctrl->type)
{
case EXPORT_TXT:
m_exp = new CTxtExport;
break;
case EXPORT_BIN:
m_exp = new CBinExport;
break;
case EXPORT_MSEED:
m_exp = new CMSeedExport;
break;
case EXPORT_SEED:
m_exp = new CSeedExport;
break;
default:
return FALSE;
}
m_filetype = pctrl->type;
GetMergeFileName(path, filename, pctrl);
char szfilename[MAX_PATH];
WcharNameToCharName(szfilename, MAX_PATH, filename, wcslen(filename));
if(FALSE == m_exp->Create(filename, pctrl))
{
if(m_plog != NULL)
{
DWORD res = GetLastError();
sprintf_s(m_plog->logString, sizeof(m_plog->logString), "file name:%s. error code:%d",
szfilename, res);
m_plog->FormatAndAppendLog(error_seed, erro_export_file_create_failed, m_plog->logString);
}
delete m_exp;
m_exp = NULL;
ret = FALSE;
}else if(m_plog != NULL)
{
SYSTEMTIME loc;
GetLocalTime(&loc);
sprintf_s(m_plog->logString, sizeof(m_plog->logString), "file name:%s."
"at time:%4d-%2d-%2d,%2d:%2d:%2d",
szfilename,
loc.wYear, loc.wMonth, loc.wDay,
loc.wHour, loc.wMinute, loc.wSecond);
m_plog->FormatAndAppendLog(info_seed, info_merge_file_created, m_plog->logString);
}
//保存日志
if(m_plog != NULL)
m_plog->SaveLog();
return ret;
}
/**
* Closes the file
*/
void FStatNotifyProvider_File::Destroy(void)
{
// Close the output file if we have one
CloseOutputFile();
}
/**
* Stop writing stats data and finalize the file
*/
void FStatNotifyProvider_BinaryFile::StopWritingStatsFile()
{
if( File != NULL )
{
FArchive& OutputFile = *File;
// Make sure the stats manager has a fresh list of descriptions for us. Note that
// this MUST happen after we've finished capturing stat data, because some stat types
// are added on-demand, such as script cycle stats
// @todo: This is a bit sketchy right here, we should avoid hitting the other provider types
GStatManager.SendNotifiersDescriptions();
// Write group descriptions
{
// Write data chunk tag for 'Script profiler data'
DWORD DataChunkTag = EStatsDataChunkTag_GroupDescriptions;
OutputFile << DataChunkTag;
/* const */ WORD GroupDescriptionCount = GroupDescriptions.Num();
OutputFile << GroupDescriptionCount;
for( WORD CurGroupIndex = 0; CurGroupIndex < GroupDescriptionCount; ++CurGroupIndex )
{
/* const */ FStatGroupDescriptionData& CurGroupDesc = GroupDescriptions( CurGroupIndex );
WORD ShortGroupID = CurGroupDesc.ID;
OutputFile << ShortGroupID;
OutputFile << CurGroupDesc.Name;
}
}
// Write stat descriptions
{
// Write data chunk tag for 'Script profiler data'
DWORD DataChunkTag = EStatsDataChunkTag_StatDescriptions;
OutputFile << DataChunkTag;
/* const */ WORD StatDescriptionCount = StatDescriptions.Num();
OutputFile << StatDescriptionCount;
for( WORD CurStatIndex = 0; CurStatIndex < StatDescriptionCount; ++CurStatIndex )
{
/* const */ FStatDescriptionData& CurStatDesc = StatDescriptions( CurStatIndex );
WORD ShortStatID = CurStatDesc.ID;
OutputFile << ShortStatID;
OutputFile << CurStatDesc.Name;
BYTE ShortStatType = CurStatDesc.StatType;
OutputFile << ShortStatType;
WORD ShortGroupID = CurStatDesc.GroupID;
OutputFile << ShortGroupID;
BYTE ShortIsScriptFunctionStat = CurStatDesc.bIsScriptFunctionStat;
OutputFile << ShortIsScriptFunctionStat;
}
}
const FString FullFileName = ArchiveFilename;
// Flush and close the file
CloseOutputFile();
warnf(TEXT("UE3Stats: done writing file [%s]"),*(FullFileName));
SendDataToPCViaUnrealConsole( TEXT("UE_PROFILER!UE3STATS:"), FullFileName );
// Decrease counter forcing scoped cycle stats to be enabled.
--GForceEnableScopedCycleStats;
debugf( TEXT( "Stats System: Finished capturing stat data." ) );
}
else
{
// File not started yet?
debugf( TEXT( "Stats System: Stats file capture hasn't been started yet." ) );
}
}
RESLT COutputReader::OpenOutputFile(TCHAR *FileName)
{
DWORD bytes;
//int i;
//SPECIESBINOUTINF speInf;
CEnvironmentData bath;
CEnvironmentData salt;
CEnvironmentData temp;
//DWORD filePointer;
//RESLT res;
//BOOL rslt;
if(m_hdl != NULL && m_hdl != INVALID_HANDLE_VALUE)
CloseOutputFile();
m_hdl = CreateFile(FileName, GENERIC_READ, NULL, NULL, OPEN_EXISTING, FILE_ATTRIBUTE_NORMAL | FILE_FLAG_RANDOM_ACCESS, 0);
if(m_hdl == INVALID_HANDLE_VALUE)
return OPENFILEREAD_ERROR;
if(FALSE == ReadFile(m_hdl, &m_sceParams, sizeof(_fSCENARIOPARAMS), &bytes, NULL))
{
CloseOutputFile();
return FILEREAD_ERROR;
}
//CloseOutputFile();
return OK;
// Not sure about what follows
# if 0
m_binOutputConfig = CFileManager::TranslateBinFileOutConfiguration(m_sceParams.binOutStateItemConfig);
// Read in the bathymetry file (if the scenario was configured to save it).
if(m_binOutputConfig.headerInf.bathyMap == TRUE && OK != (res = bath.LoadFromBinFile(m_hdl)))
{
CloseOutputFile();
return res;
}
// Read in the salinity file (if the scenario was configured to save it).
if(m_binOutputConfig.headerInf.salinityMap == TRUE && OK != (res = salt.LoadFromBinFile(m_hdl)))
{
CloseOutputFile();
return res;
}
// Read in the temperature file (if the scenario was configured to save it).
if(m_binOutputConfig.headerInf.temperatureMap == TRUE && OK != (res = temp.LoadFromBinFile(m_hdl)))
{
CloseOutputFile();
return res;
}
// Skip past statistical data if scenario was configured to save it.
if(m_binOutputConfig.headerInf.postRunAnalysis == TRUE)
{
filePointer = MySetFilePointer(m_hdl, sizeof(TAKE), FILE_CURRENT);
filePointer = MySetFilePointer(m_hdl, sizeof(TAKESTATS)*m_sceParams.numSpecies, FILE_CURRENT);
}
// Read in species model information (if the scenario was configured to save it).
if(m_binOutputConfig.headerInf.speInfAndAnimatAsscn == TRUE)
{
_ASSERT(m_speInf == NULL);
_ASSERT(m_aniAssoc == NULL);
m_speInf = new SPECIESBINOUTINF[m_sceParams.numSpecies];
m_aniAssoc = new ANIMATASSCN[m_sceParams.totalNumAnimats];
// Skip over minor species information
for(i=0; i<(int)m_sceParams.numSpecies && rslt == TRUE; i++)
{
if(FALSE == (rslt = ReadFile(m_hdl, &m_speInf[i], sizeof(SPECIESBINOUTINF), &bytes, NULL)))
return FILEREAD_ERROR;
// Skip past the behavior names that belong to this species.
filePointer = MySetFilePointer(m_hdl, __int64(m_speInf[i].description.numBehaviors) * sizeof(BEHAVIOR_NAME), FILE_CURRENT);
if(INVALID_SET_FILE_POINTER == filePointer)
return SETFILEPOINTER_ERROR;
}
// Read in animat summaries/association to species.
rslt &= ReadFile(m_hdl, m_aniAssoc, m_sceParams.totalNumAnimats * sizeof(ANIMATASSCN), &bytes, NULL);
return FILEREAD_ERROR;
}
// Skip over acoustic exposures, get the file pointer for animat states (- 1
// to number of iterations because because an initial AE isn't saved).
m_filePointerAnimats =
MySetFilePointer(m_hdl, __int64(m_sceParams.duration-1) * sizeof(ACST_SRC_STATE), FILE_CURRENT);
if(INVALID_SET_FILE_POINTER == filePointer)
return SETFILEPOINTER_ERROR;
return OK;
#endif
}
void MolecularDynamicsSimulation(void)
{
int i,j,k;
REAL ran;
// for a crash-recovery we skip the initialization and jump to the
// position right after the crash-file was written in the production run
if(ContinueAfterCrash)
{
if(SimulationStage==POSITION_INITIALIZATION) goto ContinueAfterCrashLabel1;
else if(SimulationStage==VELOCITY_EQUILIBRATION) goto ContinueAfterCrashLabel2;
else goto ContinueAfterCrashLabel3;
}
// compute gas properties
// here the pressure is converted to fugacities
ComputeGasPropertiesForAllSystems();
// open output-file
OpenOutputFile();
// print all the pre-simulations data
PrintPreSimulationStatus();
// allocate memory
SampleRadialDistributionFunction(ALLOCATE);
SampleProjectedLengthsDistributionFunction(ALLOCATE);
SampleProjectedAnglesDistributionFunction(ALLOCATE);
SampleNumberOfMoleculesHistogram(ALLOCATE);
SamplePositionHistogram(ALLOCATE);
SampleFreeEnergyProfile(ALLOCATE);
SampleEndToEndDistanceHistogram(ALLOCATE);
SampleEnergyHistogram(ALLOCATE);
SampleFrameworkSpacingHistogram(ALLOCATE);
SampleResidenceTimes(ALLOCATE);
SampleDistanceHistogram(ALLOCATE);
SampleBendAngleHistogram(ALLOCATE);
SampleDihedralAngleHistogram(ALLOCATE);
SampleAngleBetweenPlanesHistogram(ALLOCATE);
SampleMoleculePropertyHistogram(ALLOCATE);
SampleInfraRedSpectra(ALLOCATE);
SampleMeanSquaredDisplacementOrderN(ALLOCATE);
SampleVelocityAutoCorrelationFunctionOrderN(ALLOCATE);
SampleRotationalVelocityAutoCorrelationFunctionOrderN(ALLOCATE);
SampleMolecularOrientationAutoCorrelationFunctionOrderN(ALLOCATE);
SampleBondOrientationAutoCorrelationFunctionOrderN(ALLOCATE);
SampleMeanSquaredDisplacement(ALLOCATE);
SampleVelocityAutoCorrelationFunction(ALLOCATE);
SampleDensityProfile3DVTKGrid(ALLOCATE);
SampleCationAndAdsorptionSites(ALLOCATE);
SampleDcTSTConfigurationFiles(ALLOCATE);
SamplePDBMovies(ALLOCATE,-1);
// initialize
InitializesEnergiesAllSystems();
InitializeSmallMCStatisticsAllSystems();
InitializeMCMovesStatisticsAllSystems();
// compute initial energy
CalculateTotalEnergyAllSystems();
// Monte-Carlo initializing period to achieve a rapid equilibration of the positions
SimulationStage=POSITION_INITIALIZATION;
for(CurrentCycle=0;CurrentCycle<NumberOfInitializationCycles;CurrentCycle++)
{
if((CurrentCycle%PrintEvery)==0)
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
PrintIntervalStatusInit(CurrentCycle,NumberOfInitializationCycles,OutputFilePtr[CurrentSystem]);
for(j=0;j<NumberOfSystems*NumberOfComponents;j++)
{
// choose a random system
CurrentSystem=(int)(RandomNumber()*(REAL)NumberOfSystems);
for(k=0;k<MAX2(MinimumInnerCycles,NumberOfAdsorbateMolecules[CurrentSystem]);k++)
{
// choose a random component
CurrentComponent=(int)(RandomNumber()*(REAL)NumberOfComponents);
// choose any of the MC moves randomly with the selected probability
ran=RandomNumber();
if(ran<Components[CurrentComponent].ProbabilityTranslationMove)
TranslationMove();
else if(ran<Components[CurrentComponent].ProbabilityRandomTranslationMove)
RandomTranslationMove();
else if(ran<Components[CurrentComponent].ProbabilityRotationMove)
RotationMove();
else if(ran<Components[CurrentComponent].ProbabilityPartialReinsertionMove)
PartialReinsertionMove();
else if(ran<Components[CurrentComponent].ProbabilityReinsertionMove)
ReinsertionMove();
else if(ran<Components[CurrentComponent].ProbabilityReinsertionInPlaceMove)
ReinsertionInPlaceMove();
else if(ran<Components[CurrentComponent].ProbabilityReinsertionInPlaneMove)
ReinsertionInPlaneMove();
else if(ran<Components[CurrentComponent].ProbabilityIdentityChangeMove)
IdentityChangeMove();
else if(ran<Components[CurrentComponent].ProbabilitySwapMove)
{
if(RandomNumber()<0.5) SwapAddMove();
else SwapRemoveMove();
}
else if(ran<Components[CurrentComponent].ProbabilityCFSwapLambdaMove)
CFSwapLambaMove();
else if(ran<Components[CurrentComponent].ProbabilityCBCFSwapLambdaMove)
CBCFSwapLambaMove();
else if(ran<Components[CurrentComponent].ProbabilityWidomMove)
;
else if(ran<Components[CurrentComponent].ProbabilitySurfaceAreaMove)
;
else if(ran<Components[CurrentComponent].ProbabilityGibbsChangeMove)
GibbsParticleTransferMove();
else if(ran<Components[CurrentComponent].ProbabilityGibbsIdentityChangeMove)
GibbsIdentityChangeMove();
else if(ran<Components[CurrentComponent].ProbabilityCFGibbsChangeMove)
CFGibbsParticleTransferMove();
else if(ran<Components[CurrentComponent].ProbabilityCBCFGibbsChangeMove)
CBCFGibbsParticleTransferMove();
else if(ran<Components[CurrentComponent].ProbabilityParallelTemperingMove)
ParallelTemperingMove();
else if(ran<Components[CurrentComponent].ProbabilityHyperParallelTemperingMove)
HyperParallelTemperingMove();
else if(ran<Components[CurrentComponent].ProbabilityParallelMolFractionMove)
ParallelMolFractionMove();
else if(ran<Components[CurrentComponent].ProbabilityChiralInversionMove)
ChiralInversionMove();
else if(ran<Components[CurrentComponent].ProbabilityHybridNVEMove)
HybridNVEMove();
else if(ran<Components[CurrentComponent].ProbabilityHybridNPHMove)
HybridNPHMove();
else if(ran<Components[CurrentComponent].ProbabilityHybridNPHPRMove)
HybridNPHPRMove();
else if(ran<Components[CurrentComponent].ProbabilityVolumeChangeMove)
VolumeMove();
else if(ran<Components[CurrentComponent].ProbabilityBoxShapeChangeMove)
BoxShapeChangeMove();
else if(ran<Components[CurrentComponent].ProbabilityGibbsVolumeChangeMove)
GibbsVolumeMove();
else if(ran<Components[CurrentComponent].ProbabilityFrameworkChangeMove)
FrameworkChangeMove();
else if(ran<Components[CurrentComponent].ProbabilityFrameworkShiftMove)
FrameworkShiftMove();
}
}
if(CurrentCycle%PrintEvery==0)
{
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
OptimizeVolumeChangeAcceptence();
OptimizeTranslationAcceptence();
if(Framework[CurrentSystem].FrameworkModel==FLEXIBLE)
{
OptimizeFrameworkChangeAcceptence();
OptimizeFrameworkShiftAcceptence();
}
RescaleMaximumRotationAnglesSmallMC();
}
}
if((CurrentCycle>0)&&(WriteBinaryRestartFileEvery>0)&&(CurrentCycle%WriteBinaryRestartFileEvery==0))
WriteBinaryRestartFiles();
ContinueAfterCrashLabel1:;
}
// initialize
InitializesEnergiesAllSystems();
InitializeSmallMCStatisticsAllSystems();
InitializeMCMovesStatisticsAllSystems();
SimulationStage=VELOCITY_SCALING;
if(ReinitializeVelocities)
{
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
InitializeAdsorbateVelocities();
InitializeCationVelocities();
if(Framework[CurrentSystem].FrameworkModel==FLEXIBLE)
InitializeFrameworkVelocities();
RemoveVelocityDrift();
//AdjustSystemAngularRotationToZero();
}
}
//InitializeNoseHooverCurrentSystem();
InitializeNoseHooverAllSystems();
// compute initial energy
InitializeForcesAllSystems();
// Molecular-Dynamics initializing period to remove excessive kinetic energy due to
// poor equilibration of the positions (use with caution)
// Velocity-scaling scales the velocities at each time step to the desired temperature
/*
for(CurrentCycle=0;CurrentCycle<NumberOfVelocityScalingCycles;CurrentCycle++)
{
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
// scake the velocity to the exact temperature
AdjustVelocitiesToTemperature();
// regularly output system status and restart files
if(CurrentCycle%PrintEvery==0)
{
PrintIntervalStatusEquilibration(CurrentCycle,NumberOfEquilibrationCycles,OutputFilePtr[CurrentSystem]);
PrintRestartFile();
}
// evolve the system a full time-step
Integration();
}
}
*/
// set the current ensemble to the initialization ensemble
for(i=0;i<NumberOfSystems;i++)
Ensemble[i]=InitEnsemble[i];
InitializesEnergyAveragesAllSystems();
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
ReferenceEnergy[CurrentSystem]=ConservedEnergy[CurrentSystem];
Drift[CurrentSystem]=0.0;
}
// Molecular-Dynamics initializing period to achieve a rapid equilibration of the velocities
SimulationStage=VELOCITY_EQUILIBRATION;
for(CurrentCycle=0;CurrentCycle<NumberOfEquilibrationCycles;CurrentCycle++)
{
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
// regularly output system status and restart files
if(CurrentCycle%PrintEvery==0)
{
PrintIntervalStatusEquilibration(CurrentCycle,NumberOfEquilibrationCycles,OutputFilePtr[CurrentSystem]);
PrintRestartFile();
}
// insertion/deletion for the osmotic-ensemble
if(Ensemble[CurrentSystem]==MuPT)
{
CurrentComponent=(int)(RandomNumber()*NumberOfComponents);
if((CurrentCycle%(Components[CurrentComponent].SwapEvery)==0)&&
(Components[CurrentComponent].ProbabilitySwapMove>0.0))
{
if(RandomNumber()<0.5) SwapAddMove();
else SwapRemoveMove();
}
}
// evolve the system a full time-step
Integration();
// prevent heating of the core-shells
AdjustCoreShellVelocities();
// update the current energy-drift
Drift[CurrentSystem]+=fabs((ConservedEnergy[CurrentSystem]-ReferenceEnergy[CurrentSystem])/ReferenceEnergy[CurrentSystem]);
}
if((CurrentCycle>0)&&(WriteBinaryRestartFileEvery>0)&&(CurrentCycle%WriteBinaryRestartFileEvery==0))
WriteBinaryRestartFiles();
ContinueAfterCrashLabel2:;
}
// initialize sampling-routines at the start of the production run
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
Ensemble[CurrentSystem]=RunEnsemble[CurrentSystem];
ReferenceEnergy[CurrentSystem]=ConservedEnergy[CurrentSystem];
Drift[CurrentSystem]=0.0;
SampleRadialDistributionFunction(INITIALIZE);
SampleProjectedLengthsDistributionFunction(INITIALIZE);
SampleProjectedAnglesDistributionFunction(INITIALIZE);
SampleNumberOfMoleculesHistogram(INITIALIZE);
SamplePositionHistogram(INITIALIZE);
SampleFreeEnergyProfile(INITIALIZE);
SampleEndToEndDistanceHistogram(INITIALIZE);
SampleEnergyHistogram(INITIALIZE);
SampleFrameworkSpacingHistogram(INITIALIZE);
SampleResidenceTimes(INITIALIZE);
SampleDistanceHistogram(INITIALIZE);
SampleBendAngleHistogram(INITIALIZE);
SampleDihedralAngleHistogram(INITIALIZE);
SampleAngleBetweenPlanesHistogram(INITIALIZE);
SampleMoleculePropertyHistogram(INITIALIZE);
SampleInfraRedSpectra(INITIALIZE);
SampleMeanSquaredDisplacementOrderN(INITIALIZE);
SampleVelocityAutoCorrelationFunctionOrderN(INITIALIZE);
SampleRotationalVelocityAutoCorrelationFunctionOrderN(INITIALIZE);
SampleMolecularOrientationAutoCorrelationFunctionOrderN(INITIALIZE);
SampleBondOrientationAutoCorrelationFunctionOrderN(INITIALIZE);
SampleMeanSquaredDisplacement(INITIALIZE);
SampleVelocityAutoCorrelationFunction(INITIALIZE);
SampleDensityProfile3DVTKGrid(INITIALIZE);
SampleCationAndAdsorptionSites(INITIALIZE);
SampleDcTSTConfigurationFiles(INITIALIZE);
SamplePDBMovies(INITIALIZE,-1);
}
// Molecular-Dynamics production run
// loop over the amount of production cycles (MD integration steps)
SimulationStage=PRODUCTION;
for(CurrentCycle=0;CurrentCycle<NumberOfCycles;CurrentCycle++)
{
// detect erroneous chirality changes
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
CheckChiralityMolecules();
// loop over all the systems and handle one by one
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
// update all the average energies
UpdateEnergyAveragesCurrentSystem();
if(CurrentCycle%PrintPropertiesEvery==0)
PrintPropertyStatus(CurrentCycle,NumberOfCycles,OutputFilePtr[CurrentSystem]);
if(CurrentCycle%PrintEvery==0)
{
PrintIntervalStatus(CurrentCycle,NumberOfCycles,OutputFilePtr[CurrentSystem]);
PrintRestartFile();
}
// insertion/deletion for the osmotic-ensemble
if(Ensemble[CurrentSystem]==MuPT)
{
CurrentComponent=(int)(RandomNumber()*NumberOfComponents);
if((CurrentCycle%(Components[CurrentComponent].SwapEvery)==0)&&
(Components[CurrentComponent].FractionOfSwapMove>0.0))
{
if(RandomNumber()<0.5) SwapAddMove();
else SwapRemoveMove();
}
}
for(CurrentComponent=0;CurrentComponent<NumberOfComponents;CurrentComponent++)
{
if(Components[CurrentComponent].FractionOfWidomMove>0.0)
WidomMove();
}
// evolve the system a full time step
Integration();
// update the current energy-drift
Drift[CurrentSystem]+=fabs((ConservedEnergy[CurrentSystem]-ReferenceEnergy[CurrentSystem])/
ReferenceEnergy[CurrentSystem]);
if(Drift[CurrentSystem]/(CurrentCycle+1.0)>1e2)
{
fprintf(OutputFilePtr[CurrentSystem],"\n\nERROR: unstable integration (energy drift %g > 1e2, simulation stopped)\n\n",Drift[CurrentSystem]/(CurrentCycle+1.0));
fprintf(OutputFilePtr[CurrentSystem],"Check that: 1) all interaction are defined properly\n");
fprintf(OutputFilePtr[CurrentSystem]," 2) the time step is not too large\n");
fprintf(OutputFilePtr[CurrentSystem]," 3) the system is equilibrated\n\n");
fflush(OutputFilePtr[CurrentSystem]);
exit(0);
}
}
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
SampleRadialDistributionFunction(SAMPLE);
SampleProjectedLengthsDistributionFunction(SAMPLE);
SampleProjectedAnglesDistributionFunction(SAMPLE);
SampleNumberOfMoleculesHistogram(SAMPLE);
SamplePositionHistogram(SAMPLE);
SampleFreeEnergyProfile(SAMPLE);
SampleEndToEndDistanceHistogram(SAMPLE);
SampleEnergyHistogram(SAMPLE);
SampleFrameworkSpacingHistogram(SAMPLE);
SampleResidenceTimes(SAMPLE);
SampleDistanceHistogram(SAMPLE);
SampleBendAngleHistogram(SAMPLE);
SampleDihedralAngleHistogram(SAMPLE);
SampleAngleBetweenPlanesHistogram(SAMPLE);
SampleMoleculePropertyHistogram(SAMPLE);
SampleInfraRedSpectra(SAMPLE);
SampleMeanSquaredDisplacementOrderN(SAMPLE);
SampleVelocityAutoCorrelationFunctionOrderN(SAMPLE);
SampleRotationalVelocityAutoCorrelationFunctionOrderN(SAMPLE);
SampleMolecularOrientationAutoCorrelationFunctionOrderN(SAMPLE);
SampleBondOrientationAutoCorrelationFunctionOrderN(SAMPLE);
SampleMeanSquaredDisplacement(SAMPLE);
SampleVelocityAutoCorrelationFunction(SAMPLE);
SampleDensityProfile3DVTKGrid(SAMPLE);
SampleCationAndAdsorptionSites(SAMPLE);
SampleDcTSTConfigurationFiles(SAMPLE);
SamplePDBMovies(SAMPLE,-1);
}
if((CurrentCycle>0)&&(WriteBinaryRestartFileEvery>0)&&(CurrentCycle%WriteBinaryRestartFileEvery==0))
WriteBinaryRestartFiles();
ContinueAfterCrashLabel3:;
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
// regulary output sampling function
SampleRadialDistributionFunction(PRINT);
SampleProjectedLengthsDistributionFunction(PRINT);
SampleProjectedAnglesDistributionFunction(PRINT);
SampleNumberOfMoleculesHistogram(PRINT);
SamplePositionHistogram(PRINT);
SampleFreeEnergyProfile(PRINT);
SampleEndToEndDistanceHistogram(PRINT);
SampleEnergyHistogram(PRINT);
SampleFrameworkSpacingHistogram(PRINT);
SampleResidenceTimes(PRINT);
SampleDistanceHistogram(PRINT);
SampleBendAngleHistogram(PRINT);
SampleDihedralAngleHistogram(PRINT);
SampleAngleBetweenPlanesHistogram(PRINT);
SampleMoleculePropertyHistogram(PRINT);
SampleInfraRedSpectra(PRINT);
SampleMeanSquaredDisplacementOrderN(PRINT);
SampleVelocityAutoCorrelationFunctionOrderN(PRINT);
SampleRotationalVelocityAutoCorrelationFunctionOrderN(PRINT);
SampleMolecularOrientationAutoCorrelationFunctionOrderN(PRINT);
SampleBondOrientationAutoCorrelationFunctionOrderN(PRINT);
SampleMeanSquaredDisplacement(PRINT);
SampleVelocityAutoCorrelationFunction(PRINT);
SampleDensityProfile3DVTKGrid(PRINT);
SampleCationAndAdsorptionSites(PRINT);
SampleDcTSTConfigurationFiles(PRINT);
if(Movies[CurrentSystem]&&(CurrentCycle%WriteMoviesEvery[CurrentSystem]==0))
SamplePDBMovies(PRINT,-1);
}
}
if(WriteBinaryRestartFileEvery>0)
WriteBinaryRestartFiles();
// finalize and clean up
for(CurrentSystem=0;CurrentSystem<NumberOfSystems;CurrentSystem++)
{
SampleRadialDistributionFunction(FINALIZE);
SampleProjectedLengthsDistributionFunction(FINALIZE);
SampleProjectedAnglesDistributionFunction(FINALIZE);
SampleNumberOfMoleculesHistogram(FINALIZE);
SamplePositionHistogram(FINALIZE);
SampleFreeEnergyProfile(FINALIZE);
SampleEndToEndDistanceHistogram(FINALIZE);
SampleEnergyHistogram(FINALIZE);
SampleFrameworkSpacingHistogram(FINALIZE);
SampleResidenceTimes(FINALIZE);
SampleDistanceHistogram(FINALIZE);
SampleBendAngleHistogram(FINALIZE);
SampleDihedralAngleHistogram(FINALIZE);
SampleAngleBetweenPlanesHistogram(FINALIZE);
SampleMoleculePropertyHistogram(FINALIZE);
SampleInfraRedSpectra(FINALIZE);
SampleMeanSquaredDisplacementOrderN(FINALIZE);
SampleVelocityAutoCorrelationFunctionOrderN(FINALIZE);
SampleRotationalVelocityAutoCorrelationFunctionOrderN(FINALIZE);
SampleMolecularOrientationAutoCorrelationFunctionOrderN(FINALIZE);
SampleBondOrientationAutoCorrelationFunctionOrderN(FINALIZE);
SampleMeanSquaredDisplacement(FINALIZE);
SampleVelocityAutoCorrelationFunction(FINALIZE);
SampleDensityProfile3DVTKGrid(FINALIZE);
SampleCationAndAdsorptionSites(FINALIZE);
SampleDcTSTConfigurationFiles(FINALIZE);
SamplePDBMovies(FINALIZE,-1);
}
// print post-status
PrintPostSimulationStatus();
CloseOutputFile();
}
