double wwwPot(struct parameters *par,struct systemPos pos,int calcForces){
int i;
double totPot=0;
if(calcForces) /*this is not good if we want to have more than one pot at the same time!!!*/
memset(pos.xa,0,sizeof(double)*3*pos.nAtoms);
memset(pos.enPot,0,sizeof(double)*pos.nAtoms);
/*calculate forces*/
if(wwwPar.includeKeatingPot==1)
totPot+=allLoop(par,pos,calcForces,keatingInnerLoop);
else if(wwwPar.includeKeatingPot==2) /*simplified keatin */
totPot+=allLoop(par,pos,calcForces,simpKeatingInnerLoop);
else if(wwwPar.includeKeatingPot==3){ /*stix */
if(checkNgbrUpdateAll(&nd,pos,par))
updateNgbrs(&nd,pos,par);
totPot+=allLoop(par,pos,calcForces,stixInnerLoop);
}
if(wwwPar.includeRepPot){
if(checkNgbrUpdateAll(&nd,pos,par)){
updateNgbrs(&nd,pos,par);
nonNnNgbrs(&nd,pos.nAtoms); /*tkaes away first and scond ngbrs that are bonded*/
}
totPot+=allLoop(par,pos,calcForces,repulsiveInnerLoop);
}
if(wwwPar.includeSnnRep){
totPot+=allLoop(par,pos,calcForces,tabulatedRepulsiveInnerLoop);
}
if(wwwPar.includeSuboxidePot)
totPot+=allLoop(par,pos,calcForces,suboxideInnerLoop);
if(wwwPar.includeDanglbondPot)
totPot+=allLoop(par,pos,calcForces,danglBondsInnerLoop);
if(wwwPar.includeRingPot)
totPot+=wwwPar.ringPenaltyEnergy;
if(calcForces)
for(i=0;i<pos.nAtoms;i++)
if(pos.aFlag[i]==FIXED_FLAG){
pos.xa[i]=0;
pos.ya[i]=0;
pos.za[i]=0;
}
return totPot;
}
allPost::allPost(WContainerWidget *parent)
:WContainerWidget(parent)
{
allContainer =new WContainerWidget(this);
{
editButton=new WPushButton("Edit",this);
editButton->clicked().connect(this,&allPost::edit);
deleteButton= new WPushButton("delete",this);
deleteButton->clicked().connect(this,&allPost::postDelete);
dbo::Transaction T(session_);
storedPost=session_.find<Post>();
allLoop();
T.commit();
}
}
int main(int argc, char **argv){
const char *zFileToRead = 0; /* Input file. NULL for stdin */
const char *zDbName = 0; /* Name of the database file to create */
int useWithoutRowid = 0; /* True for --without-rowid */
int iMode = MODE_INSERT; /* One of MODE_xxxxx */
int iMode2; /* Mode to use for current --all iteration */
int iLoopCnt = 0; /* Which iteration when running --all */
int useNocase = 0; /* True for --nocase */
int doTrace = 0; /* True for --trace */
int showStats = 0; /* True for --stats */
int showSummary = 0; /* True for --summary */
int showTimer = 0; /* True for --timer */
int cacheSize = 0; /* Desired cache size. 0 means default */
int pageSize = 0; /* Desired page size. 0 means default */
int commitInterval = 0; /* How often to commit. 0 means never */
int noSync = 0; /* True for --nosync */
const char *zJMode = 0; /* Journal mode */
int nOp = 0; /* Operation counter */
int i, j; /* Loop counters */
sqlite3 *db; /* The SQLite database connection */
char *zSql; /* Constructed SQL statement */
sqlite3_stmt *pInsert = 0; /* The INSERT statement */
sqlite3_stmt *pUpdate = 0; /* The UPDATE statement */
sqlite3_stmt *pSelect = 0; /* The SELECT statement */
sqlite3_stmt *pDelete = 0; /* The DELETE statement */
FILE *in; /* The open input file */
int rc; /* Return code from an SQLite interface */
int iCur, iHiwtr; /* Statistics values, current and "highwater" */
FILE *pTimer = stderr; /* Output channel for the timer */
sqlite3_int64 sumCnt = 0; /* Sum in QUERY mode */
sqlite3_int64 startTime; /* Time of start */
sqlite3_int64 totalTime = 0; /* Total time */
char zInput[2000]; /* A single line of input */
/* Process command-line arguments */
for(i=1; i<argc; i++){
const char *z = argv[i];
if( z[0]=='-' ){
do{ z++; }while( z[0]=='-' );
if( strcmp(z,"without-rowid")==0 ){
useWithoutRowid = 1;
}else if( strcmp(z,"replace")==0 ){
iMode = MODE_REPLACE;
}else if( strcmp(z,"select")==0 ){
iMode = MODE_SELECT;
}else if( strcmp(z,"insert")==0 ){
iMode = MODE_INSERT;
}else if( strcmp(z,"update")==0 ){
iMode = MODE_UPDATE;
}else if( strcmp(z,"delete")==0 ){
iMode = MODE_DELETE;
}else if( strcmp(z,"query")==0 ){
iMode = MODE_QUERY;
}else if( strcmp(z,"all")==0 ){
iMode = MODE_ALL;
showTimer = -99;
}else if( strcmp(z,"nocase")==0 ){
useNocase = 1;
}else if( strcmp(z,"trace")==0 ){
doTrace = 1;
}else if( strcmp(z,"nosync")==0 ){
noSync = 1;
}else if( strcmp(z,"stats")==0 ){
showStats = 1;
}else if( strcmp(z,"summary")==0 ){
showSummary = 1;
}else if( strcmp(z,"timer")==0 ){
showTimer = i;
}else if( strcmp(z,"cachesize")==0 && i<argc-1 ){
i++;
cacheSize = atoi(argv[i]);
}else if( strcmp(z,"pagesize")==0 && i<argc-1 ){
i++;
pageSize = atoi(argv[i]);
}else if( strcmp(z,"commit")==0 && i<argc-1 ){
i++;
commitInterval = atoi(argv[i]);
}else if( strcmp(z,"journal")==0 && i<argc-1 ){
zJMode = argv[++i];
}else if( strcmp(z,"tag")==0 && i<argc-1 ){
zTag = argv[++i];
pTimer = stdout;
}else if( strcmp(z, "help")==0 || strcmp(z,"?")==0 ){
usage();
}else{
fatal_error("unknown option: \"%s\"\n"
"Use --help for a list of options\n",
argv[i]);
}
}else if( zDbName==0 ){
zDbName = argv[i];
}else if( zFileToRead==0 ){
zFileToRead = argv[i];
}else{
fatal_error("surplus argument: \"%s\"\n", argv[i]);
}
}
if( zDbName==0 ){
usage();
}
startTime = realTime();
/* Open the database and the input file */
if( zDbName[0] && strcmp(zDbName,":memory:")!=0 ){
unlink(zDbName);
}
if( sqlite3_open(zDbName, &db) ){
fatal_error("Cannot open database file: %s\n", zDbName);
}
if( zFileToRead ){
in = fopen(zFileToRead, "rb");
if( in==0 ){
fatal_error("Could not open input file \"%s\"\n", zFileToRead);
}
}else{
if( iMode==MODE_ALL ){
fatal_error("The --all mode cannot be used with stdin\n");
}
in = stdin;
}
/* Set database connection options */
if( doTrace ) sqlite3_trace(db, traceCallback, 0);
if( pageSize ){
zSql = sqlite3_mprintf("PRAGMA page_size=%d", pageSize);
sqlite3_exec(db, zSql, 0, 0, 0);
sqlite3_free(zSql);
}
if( cacheSize ){
zSql = sqlite3_mprintf("PRAGMA cache_size=%d", cacheSize);
sqlite3_exec(db, zSql, 0, 0, 0);
sqlite3_free(zSql);
}
if( noSync ) sqlite3_exec(db, "PRAGMA synchronous=OFF", 0, 0, 0);
if( zJMode ){
zSql = sqlite3_mprintf("PRAGMA journal_mode=%s", zJMode);
sqlite3_exec(db, zSql, 0, 0, 0);
sqlite3_free(zSql);
}
iLoopCnt = 0;
while( allLoop(iMode, &iLoopCnt, &iMode2, &useWithoutRowid) ){
/* Delete prior content in --all mode */
if( iMode==MODE_ALL ){
if( sqlite3_exec(db, "DROP TABLE IF EXISTS wordcount; VACUUM;",0,0,0) ){
fatal_error("Could not clean up prior iteration\n");
}
startTime = realTime();
rewind(in);
}
/* Construct the "wordcount" table into which to put the words */
if( sqlite3_exec(db, "BEGIN IMMEDIATE", 0, 0, 0) ){
fatal_error("Could not start a transaction\n");
}
zSql = sqlite3_mprintf(
"CREATE TABLE IF NOT EXISTS wordcount(\n"
" word TEXT PRIMARY KEY COLLATE %s,\n"
" cnt INTEGER\n"
")%s",
useNocase ? "nocase" : "binary",
useWithoutRowid ? " WITHOUT ROWID" : ""
);
if( zSql==0 ) fatal_error("out of memory\n");
rc = sqlite3_exec(db, zSql, 0, 0, 0);
if( rc ) fatal_error("Could not create the wordcount table: %s.\n",
sqlite3_errmsg(db));
sqlite3_free(zSql);
/* Prepare SQL statements that will be needed */
if( iMode2==MODE_QUERY ){
rc = sqlite3_prepare_v2(db,
"SELECT cnt FROM wordcount WHERE word=?1",
-1, &pSelect, 0);
if( rc ) fatal_error("Could not prepare the SELECT statement: %s\n",
sqlite3_errmsg(db));
}
if( iMode2==MODE_SELECT ){
rc = sqlite3_prepare_v2(db,
"SELECT 1 FROM wordcount WHERE word=?1",
-1, &pSelect, 0);
if( rc ) fatal_error("Could not prepare the SELECT statement: %s\n",
sqlite3_errmsg(db));
rc = sqlite3_prepare_v2(db,
"INSERT INTO wordcount(word,cnt) VALUES(?1,1)",
-1, &pInsert, 0);
if( rc ) fatal_error("Could not prepare the INSERT statement: %s\n",
sqlite3_errmsg(db));
}
if( iMode2==MODE_SELECT || iMode2==MODE_UPDATE || iMode2==MODE_INSERT ){
rc = sqlite3_prepare_v2(db,
"UPDATE wordcount SET cnt=cnt+1 WHERE word=?1",
-1, &pUpdate, 0);
if( rc ) fatal_error("Could not prepare the UPDATE statement: %s\n",
sqlite3_errmsg(db));
}
if( iMode2==MODE_INSERT ){
rc = sqlite3_prepare_v2(db,
"INSERT OR IGNORE INTO wordcount(word,cnt) VALUES(?1,1)",
-1, &pInsert, 0);
if( rc ) fatal_error("Could not prepare the INSERT statement: %s\n",
sqlite3_errmsg(db));
}
if( iMode2==MODE_UPDATE ){
rc = sqlite3_prepare_v2(db,
"INSERT OR IGNORE INTO wordcount(word,cnt) VALUES(?1,0)",
-1, &pInsert, 0);
if( rc ) fatal_error("Could not prepare the INSERT statement: %s\n",
sqlite3_errmsg(db));
}
if( iMode2==MODE_REPLACE ){
rc = sqlite3_prepare_v2(db,
"REPLACE INTO wordcount(word,cnt)"
"VALUES(?1,coalesce((SELECT cnt FROM wordcount WHERE word=?1),0)+1)",
-1, &pInsert, 0);
if( rc ) fatal_error("Could not prepare the REPLACE statement: %s\n",
sqlite3_errmsg(db));
}
if( iMode2==MODE_DELETE ){
rc = sqlite3_prepare_v2(db,
"DELETE FROM wordcount WHERE word=?1",
-1, &pDelete, 0);
if( rc ) fatal_error("Could not prepare the DELETE statement: %s\n",
sqlite3_errmsg(db));
}
/* Process the input file */
while( fgets(zInput, sizeof(zInput), in) ){
for(i=0; zInput[i]; i++){
if( !ISALPHA(zInput[i]) ) continue;
for(j=i+1; ISALPHA(zInput[j]); j++){}
/* Found a new word at zInput[i] that is j-i bytes long.
** Process it into the wordcount table. */
if( iMode2==MODE_DELETE ){
sqlite3_bind_text(pDelete, 1, zInput+i, j-i, SQLITE_STATIC);
if( sqlite3_step(pDelete)!=SQLITE_DONE ){
fatal_error("DELETE failed: %s\n", sqlite3_errmsg(db));
}
sqlite3_reset(pDelete);
}else if( iMode2==MODE_SELECT ){
sqlite3_bind_text(pSelect, 1, zInput+i, j-i, SQLITE_STATIC);
rc = sqlite3_step(pSelect);
sqlite3_reset(pSelect);
if( rc==SQLITE_ROW ){
sqlite3_bind_text(pUpdate, 1, zInput+i, j-i, SQLITE_STATIC);
if( sqlite3_step(pUpdate)!=SQLITE_DONE ){
fatal_error("UPDATE failed: %s\n", sqlite3_errmsg(db));
}
sqlite3_reset(pUpdate);
}else if( rc==SQLITE_DONE ){
sqlite3_bind_text(pInsert, 1, zInput+i, j-i, SQLITE_STATIC);
if( sqlite3_step(pInsert)!=SQLITE_DONE ){
fatal_error("Insert failed: %s\n", sqlite3_errmsg(db));
}
sqlite3_reset(pInsert);
}else{
fatal_error("SELECT failed: %s\n", sqlite3_errmsg(db));
}
}else if( iMode2==MODE_QUERY ){
sqlite3_bind_text(pSelect, 1, zInput+i, j-i, SQLITE_STATIC);
if( sqlite3_step(pSelect)==SQLITE_ROW ){
sumCnt += sqlite3_column_int64(pSelect, 0);
}
sqlite3_reset(pSelect);
}else{
sqlite3_bind_text(pInsert, 1, zInput+i, j-i, SQLITE_STATIC);
if( sqlite3_step(pInsert)!=SQLITE_DONE ){
fatal_error("INSERT failed: %s\n", sqlite3_errmsg(db));
}
sqlite3_reset(pInsert);
if( iMode2==MODE_UPDATE
|| (iMode2==MODE_INSERT && sqlite3_changes(db)==0)
){
sqlite3_bind_text(pUpdate, 1, zInput+i, j-i, SQLITE_STATIC);
if( sqlite3_step(pUpdate)!=SQLITE_DONE ){
fatal_error("UPDATE failed: %s\n", sqlite3_errmsg(db));
}
sqlite3_reset(pUpdate);
}
}
i = j-1;
/* Increment the operation counter. Do a COMMIT if it is time. */
nOp++;
if( commitInterval>0 && (nOp%commitInterval)==0 ){
sqlite3_exec(db, "COMMIT; BEGIN IMMEDIATE", 0, 0, 0);
}
}
}
sqlite3_exec(db, "COMMIT", 0, 0, 0);
sqlite3_finalize(pInsert); pInsert = 0;
sqlite3_finalize(pUpdate); pUpdate = 0;
sqlite3_finalize(pSelect); pSelect = 0;
sqlite3_finalize(pDelete); pDelete = 0;
if( iMode2==MODE_QUERY && iMode!=MODE_ALL ){
printf("%s sum of cnt: %lld\n", zTag, sumCnt);
rc = sqlite3_prepare_v2(db,"SELECT sum(cnt*cnt) FROM wordcount", -1,
&pSelect, 0);
if( rc==SQLITE_OK && sqlite3_step(pSelect)==SQLITE_ROW ){
printf("%s double-check: %lld\n", zTag,sqlite3_column_int64(pSelect,0));
}
sqlite3_finalize(pSelect);
}
if( showTimer ){
sqlite3_int64 elapseTime = realTime() - startTime;
totalTime += elapseTime;
fprintf(pTimer, "%3d.%03d wordcount", (int)(elapseTime/1000),
(int)(elapseTime%1000));
if( iMode==MODE_ALL ){
fprintf(pTimer, " %s%s\n", azMode[iMode2],
useWithoutRowid? " --without-rowid" : "");
}else{
for(i=1; i<argc; i++) if( i!=showTimer ) fprintf(pTimer," %s",argv[i]);
fprintf(pTimer, "\n");
}
}
if( showSummary ){
sqlite3_create_function(db, "checksum", -1, SQLITE_UTF8, 0,
0, checksumStep, checksumFinalize);
sqlite3_exec(db,
"SELECT 'count(*): ', count(*) FROM wordcount;\n"
"SELECT 'sum(cnt): ', sum(cnt) FROM wordcount;\n"
"SELECT 'max(cnt): ', max(cnt) FROM wordcount;\n"
"SELECT 'avg(cnt): ', avg(cnt) FROM wordcount;\n"
"SELECT 'sum(cnt=1):', sum(cnt=1) FROM wordcount;\n"
"SELECT 'top 10: ', group_concat(word, ', ') FROM "
"(SELECT word FROM wordcount ORDER BY cnt DESC, word LIMIT 10);\n"
"SELECT 'checksum: ', checksum(word, cnt) FROM "
"(SELECT word, cnt FROM wordcount ORDER BY word);\n"
"PRAGMA integrity_check;\n",
printResult, 0, 0);
}
} /* End the --all loop */
/* Close the input file after the last read */
if( zFileToRead ) fclose(in);
/* In --all mode, so the total time */
if( iMode==MODE_ALL && showTimer ){
fprintf(pTimer, "%3d.%03d wordcount --all\n", (int)(totalTime/1000),
(int)(totalTime%1000));
}
/* Database connection statistics printed after both prepared statements
** have been finalized */
if( showStats ){
sqlite3_db_status(db, SQLITE_DBSTATUS_LOOKASIDE_USED, &iCur, &iHiwtr, 0);
printf("%s Lookaside Slots Used: %d (max %d)\n", zTag, iCur,iHiwtr);
sqlite3_db_status(db, SQLITE_DBSTATUS_LOOKASIDE_HIT, &iCur, &iHiwtr, 0);
printf("%s Successful lookasides: %d\n", zTag, iHiwtr);
sqlite3_db_status(db, SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE, &iCur,&iHiwtr,0);
printf("%s Lookaside size faults: %d\n", zTag, iHiwtr);
sqlite3_db_status(db, SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL, &iCur,&iHiwtr,0);
printf("%s Lookaside OOM faults: %d\n", zTag, iHiwtr);
sqlite3_db_status(db, SQLITE_DBSTATUS_CACHE_USED, &iCur, &iHiwtr, 0);
printf("%s Pager Heap Usage: %d bytes\n", zTag, iCur);
sqlite3_db_status(db, SQLITE_DBSTATUS_CACHE_HIT, &iCur, &iHiwtr, 1);
printf("%s Page cache hits: %d\n", zTag, iCur);
sqlite3_db_status(db, SQLITE_DBSTATUS_CACHE_MISS, &iCur, &iHiwtr, 1);
printf("%s Page cache misses: %d\n", zTag, iCur);
sqlite3_db_status(db, SQLITE_DBSTATUS_CACHE_WRITE, &iCur, &iHiwtr, 1);
printf("%s Page cache writes: %d\n", zTag, iCur);
sqlite3_db_status(db, SQLITE_DBSTATUS_SCHEMA_USED, &iCur, &iHiwtr, 0);
printf("%s Schema Heap Usage: %d bytes\n", zTag, iCur);
sqlite3_db_status(db, SQLITE_DBSTATUS_STMT_USED, &iCur, &iHiwtr, 0);
printf("%s Statement Heap Usage: %d bytes\n", zTag, iCur);
}
sqlite3_close(db);
/* Global memory usage statistics printed after the database connection
** has closed. Memory usage should be zero at this point. */
if( showStats ){
sqlite3_status(SQLITE_STATUS_MEMORY_USED, &iCur, &iHiwtr, 0);
printf("%s Memory Used (bytes): %d (max %d)\n", zTag,iCur,iHiwtr);
sqlite3_status(SQLITE_STATUS_MALLOC_COUNT, &iCur, &iHiwtr, 0);
printf("%s Outstanding Allocations: %d (max %d)\n",zTag,iCur,iHiwtr);
sqlite3_status(SQLITE_STATUS_PAGECACHE_OVERFLOW, &iCur, &iHiwtr, 0);
printf("%s Pcache Overflow Bytes: %d (max %d)\n",zTag,iCur,iHiwtr);
sqlite3_status(SQLITE_STATUS_MALLOC_SIZE, &iCur, &iHiwtr, 0);
printf("%s Largest Allocation: %d bytes\n",zTag,iHiwtr);
sqlite3_status(SQLITE_STATUS_PAGECACHE_SIZE, &iCur, &iHiwtr, 0);
printf("%s Largest Pcache Allocation: %d bytes\n",zTag,iHiwtr);
}
return 0;
}
