static int
seekChars(void* state, long offset, int whence) {
long absPos;
char* pszError;
switch (whence) {
case SEEK_SET:
absPos = offset;
storagePosition(&pszError, (int)state, absPos);
break;
case SEEK_END:
absPos = sizeOfFile(state) + offset;
storagePosition(&pszError, (int)state, absPos);
break;
case SEEK_CUR:
absPos = storageRelativePosition(&pszError, (int)state, offset);
break;
default:
return -1;
}
storageFreeError(pszError);
return absPos;
}
char *readFile(const char *file)
{
FILE *f = openOrDie(file,"r");
int N = sizeOfFile(file);
char *str =(char *) malloc(N+1);
fread(str,N,1,f);
str[N]=0;
return str;
}
void InvertedIndex(void){
listOfCollection = CollectionToList();
N = Length(listOfCollection);
int L = LengthForMalloc(listOfCollection);
ptr = malloc(sizeof(BSTree) * L);
for(int i = 0; i < N; i++) {
url = valueReturn(listOfCollection,i);
urltx = strcat(url,txt);
f = fopen(urltx, "r");
sizefile = fopen(urltx, "r");
size = sizeOfFile(sizefile);
Q = getBSTree(f,size);
ptr[i]= Q;
fclose(f);
fclose(sizefile);
}
WithoutTxt = CollectionToList();
AllWords = AllWordsToList(N,listOfCollection,WithoutTxt);
int numberofWords = Length(AllWords);
FILE *Inverted = fopen("Inverted.txt","w");
for (int test = 0; test <= numberofWords; test++){
searchTerm= valueReturn(AllWords, test);
fprintf(Inverted, "%s",searchTerm);
for(int iterator = 0; iterator <= N; iterator++){
// Set the search term as the term returned by ALL
found = BSTreeFind(ptr[iterator],searchTerm);
if(found == 1){
URLname = valueReturn(WithoutTxt, iterator);
fprintf(Inverted," %s", URLname);
}
else{
// Do nothing
}
}
fprintf(Inverted,"\n");
}
}
/* If the jar size is less than zero it is an error code. */
long
midpGetJarSize(void* handle) {
MidpJarInfo* pJarInfo = (MidpJarInfo*)handle;
long size;
size = sizeOfFile(pJarInfo->fileObj.state);
if (size < 0) {
return MIDP_JAR_IO_ERROR;
}
return size;
}
unsigned int* count_From_File(FILE* fp)
{
char buf[1000];
//Make an array to hold all the charcters in the string
unsigned int i;
unsigned int* characters = (unsigned int*)malloc(sizeof(unsigned int)*256);
//Initialize the array and count the number of characters
memset(characters,0,256);
int j;
//Get the file size in bytes
int fileSizeLeft = sizeOfFile(fp);
int numReads = 0;
if(fileSizeLeft%1000 != 0)
{
numReads = fileSizeLeft/1000 + 1;
}
else
{
numReads = fileSizeLeft/1000;
}
for(j=0;j<numReads;j++)
{
if(fileSizeLeft < 1000)
{
fread(buf, sizeof(char),fileSizeLeft, fp);
count_Characters(buf, characters, fileSizeLeft);
}
else
{
fread(buf, sizeof(char),1000, fp);
count_Characters(buf, characters, 1000);
}
fileSizeLeft -= 1000;
}
return characters;
}
void loadParametersFile(const char *fname,
Parameters *parameters,
const char *distanceUnits,
const char *energyUnits)
{
Integer N = sizeOfFile(fname);
char Error[256];
FILE *f=fopen(fname,"r");
if(!f)
{ sprintf(Error,"could not open file %s",fname);
throw new Exception(NULL,Error);
}
char *str = (char *)malloc(N+1);
fread(str,1,N,f);
str[N]=0;
fclose(f);
StringParser sp(str);
ParseParameters parseParameters(distanceUnits,energyUnits,parameters);
Integer line,col;
if(!parseParameters(&sp))
{ char expected[512];
parseParameters.getExpected(expected,512);
calculateLineAndCol( str, //const char *text,
parseParameters.getErrorPos(),//const char *pos,
&line, //Integer *line, //out
&col //Integer *col //out
);
char Error[512];
sprintf(Error,"File %s: Parse error at line %d col %d: %s",fname,(int)line,(int)col,expected);
throw new Exception(NULL,Error);
}
}
/* Send a file across the network. The filename argument
* will be sent to indicate to the other side what it should
* be saved as. */
int writeFile(BIO *conn, char *filename, char *writeName) {
//if no alternate name supplied, just use it's actual name
if(writeName == NULL) writeName = filename;
FILE *ifp = fopen(filename, "rb");
if(ifp == NULL) {
perror("writeFile");
//send NO_SUCH_FILE as the file length to indicate file is not coming
writeInt(conn, NO_SUCH_FILE);
return NO_SUCH_FILE;
}
//send the file length in 4 bytes
int fileSize = sizeOfFile(filename);
if(writeInt(conn, fileSize) == -1) return -1;
if(fileSize == -1) return -1;
//send the filename first in a simple packet
if(writeString(conn, writeName) < 1) return -1;
/* Now transfer the file */
char fileBuffer[BUFSIZ];
while(fileSize > 0) {
//read a chunk
int numRead = fread(fileBuffer, 1, BUFSIZ, ifp);
if(numRead == 0) break;
//send that chunk over the network
int status = writeAll(conn, fileBuffer, numRead);
if(status < 1) return status;
fileSize -= numRead;
}
if(fileSize != 0) {
fprintf(stderr, "writeFile(): fileSize non-zero after sending. Incomplete??\n");
return -1;
}
return 1;
}
void inputToOutputFile(FILE* input, FILE* output, charTranslation* characters)
{
char buffer[1000];
size_t fileSize = sizeOfFile(input);
unsigned int num_chars = fileSize,i,j, numReads = fileSize/1000 +(fileSize%1000==0?0:1), charsToRead;
std::vector <bool> writeToFile;
for(i=0;i<numReads;i++)
{
if(fileSize>=1000)
{
charsToRead = 1000;
}
else
{
charsToRead = fileSize;
}
for(j=0;j<charsToRead;j++)
{
fread(buffer, sizeof(char),charsToRead, input );
writeToFile.insert(writeToFile.end(), characters[buffer[j]].v->begin(), characters[buffer[j]].v->end());
}
fileSize-=1000;
}
writeBoolVectorToFile(writeToFile,output);
return;
}
int
main(int argc, char **argv) {
int error = 0;
readBuffer *B = 0L;
size_t L = 0;
size_t H = 0;
size_t R = 0;
// If we are given a file, use that, otherwise, use ourself.
//
filename = argv[argc-1];
L = sizeOfFile(filename);
H = L/2;
R = L - H;
fprintf(stderr, "L=%d H=%d R=%d\n", L, H, R);
// Suck in the whole file, compute the correct md5 checksum on it
//
char *c = new char [L];
FILE *F = fopen(filename, "r");
fread(c, sizeof(char), L, F);
fclose(F);
full = md5_string(0L, c, L);
part = md5_string(0L, c+H, R);
delete [] c;
B = new readBuffer(filename, 999);
error += doTest(B, full, "#1 (read)");
B->seek(0);
error += doTest(B, full, "#2 (seek)");
B->seek(H);
error += doTest(B, part, "#2 (seek half)");
delete B;
B = new readBuffer(filename, 0);
error += doTest(B, full, "#3 (mmap)");
B->seek(0);
error += doTest(B, full, "#2 (mmap seek)");
B->seek(H);
error += doTest(B, part, "#2 (mmap seek half)");
delete B;
B = new readBuffer(filename, 0);
error += doTestRead(B, full, 10000, "#4 (read buffer=mmap readsize=10000)");
delete B;
B = new readBuffer(filename, 100);
error += doTestRead(B, full, 10000, "#4 (read buffer=100 readsize=10000)");
delete B;
B = new readBuffer(filename, 2000);
error += doTestRead(B, full, 1000, "#4 (read buffer=2000 readsize=1000)");
delete B;
B = new readBuffer(filename, L);
error += doTestRead(B, full, L+1000, "#5 (read buffer=filesize readsize=filesize+1000)");
delete B;
return(error);
}
int main(){
int N_nodes = sizeOfFile("nodepos.dat",2);
int N_patch = sizeOfFile("patch_node.dat",3);
InstArry(N_nodes,N_patch);
readNodePos();
readpatchNode();
int curnum = 0;
for(int i=1;i<=N_patch;i++){
for(int j=1;j<=3;j++){
curnum = (i-1)*3+j;
edgeInfo[curnum][1] = i;
edgeInfo[curnum][2] = j;
if (patchNode[i][next(j)]<patchNode[i][next(next(j))]){
edgeInfo[curnum][3] = patchNode[i][next(j)];
edgeInfo[curnum][4] = patchNode[i][next(next(j))];
}else{
edgeInfo[curnum][3] = patchNode[i][next(next(j))];
edgeInfo[curnum][4] = patchNode[i][next(j)];
}
}
}
sortArry(N_patch);
edgeLink[1][1] = edgeInfo[1][3];
edgeLink[1][2] = edgeInfo[1][4];
patch_edge[edgeInfo[1][1]][edgeInfo[1][2]] = 1;
int N_edge = 1;
for(int i=2;i<=3*N_patch;i++){
if((edgeInfo[i][3]!=edgeInfo[i-1][3])||(edgeInfo[i][4]!=edgeInfo[i-1][4])){
N_edge++;
edgeLink[i][1] = edgeInfo[i][3];
edgeLink[i][2] = edgeInfo[i][4];
patch_edge[edgeInfo[i][1]][edgeInfo[i][2]] = N_edge;
}else{
patch_edge[edgeInfo[i][1]][edgeInfo[i][2]] = N_edge;
}
}
int Nb = 0;
InstArryAdd(N_patch,N_edge,Nb);
CalcEFieldPos(N_edge,N_patch);
CalcHfieldPos(N_edge,N_patch, 0.01);
//Output all the data (test)
writeGrid("pos_nodes.dat","vertiic.dat",N_nodes,N_patch);
writeFiledPos(N_edge,N_patch);
//form a general matrix of coefs
for(int i = 1;i<=N_patch;i++){
// all electric field global numbers corresponding to givern patch
for(int j=1;j<=3;j++){
coefMat[i][2*j-1] = 2*patch_edge[i][j]-1;
coefMat[i][2*j] = 2*patch_edge[i][j];
}
coefMat[i][7] = 2*N_edge+2*i-1;
coefMat[i][8] = 2*N_edge+2*i;
for(int j=1;j<=3;j++){
if (PointInTriangle(i, 4*patch_edge[i][j]-3)== true){
coefMat[i][2*(j+4)-1] = 4*patch_edge[i][j]-3;
} else{
coefMat[i][2*(j+4)-1] = 4*patch_edge[i][j]-2;
}
if (PointInTriangle(i, 4*patch_edge[i][j]-1)== true){
coefMat[i][2*(j+4)] = 4*patch_edge[i][j]-1;
} else{
coefMat[i][2*(j+4)] = 4*patch_edge[i][j];
}
}
coefMat[i][15] = 4*N_edge+4*i-3;
coefMat[i][16] = 4*N_edge+4*i-2;
coefMat[i][17] = 4*N_edge+4*i-1;
coefMat[i][18] = 4*N_edge+4*i;
// area of the triangle
double x1 = nodePos[edgeLinkS[patch_edge[i][2]][2]][1];
double y1 = nodePos[edgeLinkS[patch_edge[i][2]][2]][2];
double x2 = nodePos[edgeLinkS[patch_edge[i][3]][2]][1];
double y2 = nodePos[edgeLinkS[patch_edge[i][3]][2]][2];
double x3 = nodePos[edgeLinkS[patch_edge[i][1]][2]][1];
double y3 = nodePos[edgeLinkS[patch_edge[i][1]][2]][2];
area[i] = fabs(x1*(y2-y3)+x2*(y3-y1)+x3*(y1-y2));
//area[i] =x1;
}
ofstream out1;
out1.open("Matrix.dat");
for(int i = 1;i<=N_patch;i++){
out1<<i<<" "<<coefMat[i][1]<<" "<<coefMat[i][2]<<" "<<coefMat[i][3]<<" "<<coefMat[i][4]<<" "<<coefMat[i][5]<<" "<<coefMat[i][6]<<" "<<coefMat[i][7]<<" "<<coefMat[i][8]<<" "<<coefMat[i][9]<<" "<<coefMat[i][10]<<" "<<coefMat[i][11]<<" "<<coefMat[i][12]<<" "<<coefMat[i][13]<<" "<<coefMat[i][14]<<" "<<coefMat[i][15]<<" "<<coefMat[i][16]<<" "<<coefMat[i][17]<<" "<<coefMat[i][18]<<" "<<area[i]<<endl;
//out1<<i<<" "<<nodePos[edgeLinkS[patch_edge[i][2]][2]][2]<<" "<<nodePos[edgeLinkS[patch_edge[i][1]][1]][2]<<" "<<nodePos[edgeLinkS[patch_edge[i][1]][2]][2]<<endl;
}
return 0;
}
void parseCommandArguments(
int argc, // in
char *argv[], //in
Parameters *params, //in/out
char *paramFile, //out
char *additionalParams, //out
char *Error, // aux
char *prefix //out
)
{
additionalParams[0]=0;
if(argc<2)
{
puts("Usage: ./calculateFreeEnergy prefix [parameters.txt] [Additional parameters string]");
puts("For proper work of the program one shoud have the following files:");
puts("\t- ${prefix}gamma${site}.3d");
puts("\t- ${prefix}c${site}.3d");
puts("\t- ${prefix}clong${site}.3d");
puts("\t- ${prefix}X.grd");
puts("\t- ${prefix}Y.grd");
puts("\t- ${prefix}Z.grd");
puts("If no parameters file is given, the file ${prefix}_parameters.txt is used");
throw new Exception(NULL,"incorrect command line arguments");
return;
}
strcpy(prefix,argv[1]);
if(argc>2)
strcpy(paramFile,argv[2]);
else
sprintf(paramFile,"%sparameters.txt",prefix);
if(argc>3)
{
strcpy(additionalParams,argv[3]);
}
Integer L=sizeOfFile(paramFile);
FILE *f=fopen(paramFile,"r");
if(L==0 || f==NULL)
{
sprintf(Error,"Cannot read parameters form file %s",paramFile);
throw new Exception(NULL,Error);
}
char *str = (char*)malloc(L+1);
fread(str,1,L,f);
fclose(f);
StringParser spFile(str);
ParseParameters parseParameters("Bohr", //const char *distanceUnits,
"Hartree", //const char * energyUnits,
params //Parameters *parameters
);
parseParameters.parse(&spFile);
free(str);
StringParser spArg(additionalParams);
parseParameters.parse(&spArg);
}
// Main Function.
int main(void)
{
int fd,c, res;
struct termios oldtio,newtio;
char buf[256];
// File variables.
FILE *filefp = NULL;
unsigned int fileSize = 0;
int bytesRead = 0;
char message[] = "Hello There stranger. This is a test.\n";
char temp;
broadCastPacket_t packet;
fd = open(XBEEPORT, O_RDWR | O_NOCTTY );
if (fd <0) {perror(XBEEPORT); exit(-1); }
tcgetattr(fd,&oldtio); /* save current port settings */
bzero(&newtio, sizeof(newtio));
newtio.c_cflag = BAUDRATE | CRTSCTS | CS8 | CLOCAL | CREAD;
newtio.c_iflag = IGNPAR;
newtio.c_oflag = 0;
/* set input mode (non-canonical, no echo,...) */
newtio.c_lflag = 0;
newtio.c_cc[VTIME] = 0; /* inter-character timer unused */
newtio.c_cc[VMIN] = 1; /* blocking read until 5 chars received */
tcflush(fd, TCIFLUSH);
tcsetattr(fd,TCSANOW,&newtio);
// Open file for reading binary
filefp = fopen(FILENAME, "rb");
if (filefp == NULL)
{
fprintf(stderr, "Could not open file %s\n", FILENAME);
exit(1);
}
fileSize = sizeOfFile(filefp);
buf[0] = 'P';
buf[1] = 'A';
buf[2] = 'C';
buf[3] = 1; // 1 indicates file transfer packet.
buf[4] = strlen(message); // copy size of file.
write(fd,buf,5); // send header.
// now send payload
write(fd,message,strlen(message));
// now send payload
//res = write(fd,"abcdh",5);
/*
while (!feof(filefp)) {
// Send a file over serial...
bytesRead = readFileBytes(filefp, buf,255);
write(fd,buf,bytesRead);
}
*/
tcsetattr(fd,TCSANOW,&oldtio); // restore old port settings.
return 0;
}
int clientUploadFile(BIO *conn, char *filename) {
/* CALCULATE AND STORE ANY RECORDS OF THIS FILE WE NEED
* BEFORE UPLOADING IT */
FILE *ifp = fopen(filename, "rb");
if ( ifp == NULL ) return NO_SUCH_FILE;
//generate key and iv for encryption
unsigned char *key = randomBytes(32);
unsigned char *iv = randomBytes(32);
//encrypt the file
int status = encryptFile(filename, TEMP_ENCRYPTED_FILENAME, key, iv);
if(status == -1) {
fprintf(stderr, "Failed to encrypt %s in clientUploadFile()\n", filename);
return -1;
}
//we need to store NUM_HASHES salts and digests for later verification
unsigned char *salts[NUM_HASHES];
unsigned char *hashes[NUM_HASHES];
for(int i=0; i<NUM_HASHES; ++i) {
//generate a random salt
salts[i] = randomBytes(SALT_LENGTH);
//compute the digest for the file with that salt
hashes[i] = calculateMD5(TEMP_ENCRYPTED_FILENAME, salts[i], SALT_LENGTH);
if(hashes[i] == NULL) {
fprintf(stderr, "Failed to calculate digest in clientUploadFile()\n");
return -1;
}
}
//store all this data for later
status = addRecord(filename, 0, hashes, salts, key, iv);
if(status == -1) {
fprintf(stderr, "addRecord() failed for in clientUploadFile()\n");
return -1;
}
//free the memory we allocated above
for(int i=0; i < NUM_HASHES; ++i) {
free(salts[i]);
free(hashes[i]);
}
free(key);
free(iv);
/* START THE ACTUAL COMMUNICATION WITH THE SERVER */
//send the code which causes the server to call serverUploadFile()
if(writeInt(conn, UPLOAD_FILE_CODE) == -1) return -1;
//send the fileSize
int fileSize = sizeOfFile(TEMP_ENCRYPTED_FILENAME);
if(writeInt(conn, fileSize) == -1) return -1;
printf("NOTE: Original size: %f MB. Encrypted size: %f MB.\n", (double)sizeOfFile(filename)/MEGABYTE, (double)fileSize/MEGABYTE);
//wait for an int telling us the balance owing
unsigned int fee = readInt(conn);
if(fee > 0) {
printf("Purchase %d more cloud dollar(s) to upload this file.\n", fee);
removeRecord(filename);
return -1;
}
else if(fee < 0) return -1;
//send the file
if(writeFile(conn, TEMP_ENCRYPTED_FILENAME, filename) < 1) return -1;
unlink( TEMP_ENCRYPTED_FILENAME );
printf("Succesfully uploaded the file.\n");
return 0;
}
