Beispiel #1
0
void rdfs(int u) {
    visited[u] = timestamp;
    if (match_x[u] != -1) {
        for (int v : rgraph[match_x[u]]) {
            if (visited[v] != timestamp) {
                parent[v] = u;
                via[v] = match_x[u];
                rdfs(v);
            }
        }
    }
}
Beispiel #2
0
void rdfs(int v, int k)
{
    used[v] = true;
    cmp[v] = k;
    for(size_t index=0; index<rG[v].size(); index++)
    {
        if(!used[rG[v][index]])
        {
            rdfs(rG[v][index]);
        }
    }
}
Beispiel #3
0
int solve()
{
	memset(used,0,sizeof(used));
	vs.clear();
	for(int v=1;v<=N;v++)
		if(!used[v]) dfs(v);
	memset(used,0,sizeof(used));
	int k=0;
	for(int i=vs.size()-1;i>=0;i--)
		if(!used[vs[i]]) rdfs(vs[i],k++);
	return k;
}
int scc() {
    memset(used,0,sizeof(used));
    vs.clear();
    for(int v = 0 ; v < V ; v++) {
        if(!used[v]) dfs(v);
    }
    memset(used,0,sizeof(used));
    int k = 0;
    for(int i = vs.size() - 1 ; i >= 0 ; i--) {
        if(!used[vs[i]]) rdfs(vs[i],k++);
    }
    return k;
}
Beispiel #5
0
void rdfs(int s, int c, int t)
{
	int i;
  vis[s] = c;
	if (asg[s]!=0 && asg[s]!=t) {
		nosat = 1;
	}
	asg[s] = t;
	asg[s^1] = -t;
    for (i=0;i<2*n;i++)
        if (A[i][s] && !vis[i])
            rdfs(i, c, t);
}
Beispiel #6
0
/*
 * allocate a block or frag
 */
daddr64_t
alloc(int size, int mode)
{
	int i, frag;
	daddr64_t d, blkno;

	rdfs(fsbtodb(&sblock, cgtod(&sblock, 0)), sblock.fs_cgsize,
	    (char *)&acg);
	if (acg.cg_magic != CG_MAGIC) {
		warnx("cg 0: bad magic number");
		return (0);
	}
	if (acg.cg_cs.cs_nbfree == 0) {
		warnx("first cylinder group ran out of space");
		return (0);
	}
	for (d = 0; d < acg.cg_ndblk; d += sblock.fs_frag)
		if (isblock(&sblock, cg_blksfree(&acg), d / sblock.fs_frag))
			goto goth;
	warnx("internal error: can't find block in cyl 0");
	return (0);
goth:
	blkno = fragstoblks(&sblock, d);
	clrblock(&sblock, cg_blksfree(&acg), blkno);
	acg.cg_cs.cs_nbfree--;
	sblock.fs_cstotal.cs_nbfree--;
	fscs[0].cs_nbfree--;
	if (mode & IFDIR) {
		acg.cg_cs.cs_ndir++;
		sblock.fs_cstotal.cs_ndir++;
		fscs[0].cs_ndir++;
	}
	if (Oflag <= 1) {
		cg_blktot(&acg)[cbtocylno(&sblock, d)]--;
		cg_blks(&sblock, &acg, cbtocylno(&sblock, d))
		    [cbtorpos(&sblock, d)]--;
	}
	if (size != sblock.fs_bsize) {
		frag = howmany(size, sblock.fs_fsize);
		fscs[0].cs_nffree += sblock.fs_frag - frag;
		sblock.fs_cstotal.cs_nffree += sblock.fs_frag - frag;
		acg.cg_cs.cs_nffree += sblock.fs_frag - frag;
		acg.cg_frsum[sblock.fs_frag - frag]++;
		for (i = frag; i < sblock.fs_frag; i++)
			setbit(cg_blksfree(&acg), d + i);
	}
	wtfs(fsbtodb(&sblock, cgtod(&sblock, 0)), sblock.fs_cgsize,
	    (char *)&acg);
	return (d);
}
Beispiel #7
0
/*
 * Allocate an inode on the disk
 */
void
iput(union dinode *ip, ino_t ino)
{
	daddr64_t d;

	if (Oflag <= 1)
		ip->dp1.di_gen = (u_int32_t)arc4random();
	else
		ip->dp2.di_gen = (u_int32_t)arc4random();

	rdfs(fsbtodb(&sblock, cgtod(&sblock, 0)), sblock.fs_cgsize,
	    (char *)&acg);
	if (acg.cg_magic != CG_MAGIC)
		errx(41, "cg 0: bad magic number");

	acg.cg_cs.cs_nifree--;
	setbit(cg_inosused(&acg), ino);

	wtfs(fsbtodb(&sblock, cgtod(&sblock, 0)), sblock.fs_cgsize,
	    (char *)&acg);

	sblock.fs_cstotal.cs_nifree--;
	fscs[0].cs_nifree--;
	if (ino >= sblock.fs_ipg * sblock.fs_ncg)
		errx(32, "fsinit: inode value %d out of range", ino);
	d = fsbtodb(&sblock, ino_to_fsba(&sblock, ino));
	rdfs(d, sblock.fs_bsize, iobuf);

	if (Oflag <= 1)
		((struct ufs1_dinode *)iobuf)[ino_to_fsbo(&sblock, ino)] =
		    ip->dp1;
	else
		((struct ufs2_dinode *)iobuf)[ino_to_fsbo(&sblock, ino)] =
		    ip->dp2;

	wtfs(d, sblock.fs_bsize, iobuf);
}
Beispiel #8
0
int solve2sat()
{
	int i, cmpcol;
	nosat = 0;
    /* Forward */
    dfsclear();
    push = 0;
    for (i=0;i<2*n;i++)
        if (!vis[i])
            dfs(i);
    /* Backward */
    dfsclear();
    cmpcol = 1;
    while (push && !nosat) {
			if (!vis[stack[push-1]]) {
      		rdfs(stack[push-1], cmpcol, asg[stack[push-1]]!=0?asg[stack[push-1]]:-1);
        cmpcol++;
    		}
      push--;
    }
	return !nosat;
}
Beispiel #9
0
int scc()
{
    memset(used, 0, sizeof(used));
    vs.clear();
    for(size_t v=0; v<V; v++)
    {
        if(!used[v])
        {
            dfs[v];
        }
    }
    memset(used, 0, sizeof(used));
    int k = 0;
    for(size_t index=vs.size()-1; index>=0; i--)
    {
        if(!used[vs[i]])
        {
            rdfs(vs[i], k++);
        }
    }
    return k;
}
Beispiel #10
0
/*
 * Here we actually start growing the file system. We basically read the
 * cylinder summary from the first cylinder group as we want to update
 * this on the fly during our various operations. First we handle the
 * changes in the former last cylinder group. Afterwards we create all new
 * cylinder groups.  Now we handle the cylinder group containing the
 * cylinder summary which might result in a relocation of the whole
 * structure.  In the end we write back the updated cylinder summary, the
 * new superblock, and slightly patched versions of the super block
 * copies.
 */
static void
growfs(int fsi, int fso, unsigned int Nflag)
{
	DBG_FUNC("growfs")
	time_t modtime;
	uint cylno;
	int i, j, width;
	char tmpbuf[100];

	DBG_ENTER;

	time(&modtime);

	/*
	 * Get the cylinder summary into the memory.
	 */
	fscs = (struct csum *)calloc((size_t)1, (size_t)sblock.fs_cssize);
	if (fscs == NULL)
		errx(1, "calloc failed");
	for (i = 0; i < osblock.fs_cssize; i += osblock.fs_bsize) {
		rdfs(fsbtodb(&osblock, osblock.fs_csaddr +
		    numfrags(&osblock, i)), (size_t)MIN(osblock.fs_cssize - i,
		    osblock.fs_bsize), (void *)(((char *)fscs) + i), fsi);
	}

#ifdef FS_DEBUG
	{
		struct csum *dbg_csp;
		u_int32_t dbg_csc;
		char dbg_line[80];

		dbg_csp = fscs;

		for (dbg_csc = 0; dbg_csc < osblock.fs_ncg; dbg_csc++) {
			snprintf(dbg_line, sizeof(dbg_line),
			    "%d. old csum in old location", dbg_csc);
			DBG_DUMP_CSUM(&osblock, dbg_line, dbg_csp++);
		}
	}
#endif /* FS_DEBUG */
	DBG_PRINT0("fscs read\n");

	/*
	 * Do all needed changes in the former last cylinder group.
	 */
	updjcg(osblock.fs_ncg - 1, modtime, fsi, fso, Nflag);

	/*
	 * Dump out summary information about file system.
	 */
#ifdef FS_DEBUG
#define B2MBFACTOR (1 / (1024.0 * 1024.0))
	printf("growfs: %.1fMB (%jd sectors) block size %d, fragment size %d\n",
	    (float)sblock.fs_size * sblock.fs_fsize * B2MBFACTOR,
	    (intmax_t)fsbtodb(&sblock, sblock.fs_size), sblock.fs_bsize,
	    sblock.fs_fsize);
	printf("\tusing %d cylinder groups of %.2fMB, %d blks, %d inodes.\n",
	    sblock.fs_ncg, (float)sblock.fs_fpg * sblock.fs_fsize * B2MBFACTOR,
	    sblock.fs_fpg / sblock.fs_frag, sblock.fs_ipg);
	if (sblock.fs_flags & FS_DOSOFTDEP)
		printf("\twith soft updates\n");
#undef B2MBFACTOR
#endif /* FS_DEBUG */

	/*
	 * Now build the cylinders group blocks and
	 * then print out indices of cylinder groups.
	 */
	printf("super-block backups (for fsck_ffs -b #) at:\n");
	i = 0;
	width = charsperline();

	/*
	 * Iterate for only the new cylinder groups.
	 */
	for (cylno = osblock.fs_ncg; cylno < sblock.fs_ncg; cylno++) {
		initcg(cylno, modtime, fso, Nflag);
		j = sprintf(tmpbuf, " %jd%s",
		    (intmax_t)fsbtodb(&sblock, cgsblock(&sblock, cylno)),
		    cylno < (sblock.fs_ncg - 1) ? "," : "" );
		if (i + j >= width) {
			printf("\n");
			i = 0;
		}
		i += j;
		printf("%s", tmpbuf);
		fflush(stdout);
	}
	printf("\n");

	/*
	 * Do all needed changes in the first cylinder group.
	 * allocate blocks in new location
	 */
	updcsloc(modtime, fsi, fso, Nflag);

	/*
	 * Now write the cylinder summary back to disk.
	 */
	for (i = 0; i < sblock.fs_cssize; i += sblock.fs_bsize) {
		wtfs(fsbtodb(&sblock, sblock.fs_csaddr + numfrags(&sblock, i)),
		    (size_t)MIN(sblock.fs_cssize - i, sblock.fs_bsize),
		    (void *)(((char *)fscs) + i), fso, Nflag);
	}
	DBG_PRINT0("fscs written\n");

#ifdef FS_DEBUG
	{
		struct csum	*dbg_csp;
		u_int32_t	dbg_csc;
		char	dbg_line[80];

		dbg_csp = fscs;
		for (dbg_csc = 0; dbg_csc < sblock.fs_ncg; dbg_csc++) {
			snprintf(dbg_line, sizeof(dbg_line),
			    "%d. new csum in new location", dbg_csc);
			DBG_DUMP_CSUM(&sblock, dbg_line, dbg_csp++);
		}
	}
#endif /* FS_DEBUG */

	/*
	 * Now write the new superblock back to disk.
	 */
	sblock.fs_time = modtime;
	wtfs(sblockloc, (size_t)SBLOCKSIZE, (void *)&sblock, fso, Nflag);
	DBG_PRINT0("sblock written\n");
	DBG_DUMP_FS(&sblock, "new initial sblock");

	/*
	 * Clean up the dynamic fields in our superblock copies.
	 */
	sblock.fs_fmod = 0;
	sblock.fs_clean = 1;
	sblock.fs_ronly = 0;
	sblock.fs_cgrotor = 0;
	sblock.fs_state = 0;
	memset((void *)&sblock.fs_fsmnt, 0, sizeof(sblock.fs_fsmnt));
	sblock.fs_flags &= FS_DOSOFTDEP;

	/*
	 * XXX
	 * The following fields are currently distributed from the superblock
	 * to the copies:
	 *     fs_minfree
	 *     fs_rotdelay
	 *     fs_maxcontig
	 *     fs_maxbpg
	 *     fs_minfree,
	 *     fs_optim
	 *     fs_flags regarding SOFTPDATES
	 *
	 * We probably should rather change the summary for the cylinder group
	 * statistics here to the value of what would be in there, if the file
	 * system were created initially with the new size. Therefor we still
	 * need to find an easy way of calculating that.
	 * Possibly we can try to read the first superblock copy and apply the
	 * "diffed" stats between the old and new superblock by still copying
	 * certain parameters onto that.
	 */

	/*
	 * Write out the duplicate super blocks.
	 */
	for (cylno = 0; cylno < sblock.fs_ncg; cylno++) {
		wtfs(fsbtodb(&sblock, cgsblock(&sblock, cylno)),
		    (size_t)SBLOCKSIZE, (void *)&sblock, fso, Nflag);
	}
	DBG_PRINT0("sblock copies written\n");
	DBG_DUMP_FS(&sblock, "new other sblocks");

	DBG_LEAVE;
	return;
}
Beispiel #11
0
void
mkfs(struct partition *pp, char *fsys, int fi, int fo, mode_t mfsmode,
    uid_t mfsuid, gid_t mfsgid)
{
	time_t utime;
	quad_t sizepb;
	int i, j, width, origdensity, fragsperinode, minfpg, optimalfpg;
	int lastminfpg, mincylgrps;
	long cylno, csfrags;
	char tmpbuf[100];	/* XXX this will break in about 2,500 years */

	if ((fsun = calloc(1, sizeof (union fs_u))) == NULL ||
	    (cgun = calloc(1, sizeof (union cg_u))) == NULL)
		err(1, "calloc");

#ifndef STANDALONE
	time(&utime);
#endif
	if (mfs) {
		quad_t sz = (quad_t)fssize * sectorsize;
		if (sz > SIZE_T_MAX) {
			errno = ENOMEM;
			err(12, "mmap");
		}
		membase = mmap(NULL, sz, PROT_READ|PROT_WRITE,
		    MAP_ANON|MAP_PRIVATE, -1, (off_t)0);
		if (membase == MAP_FAILED)
			err(12, "mmap");
		madvise(membase, sz, MADV_RANDOM);
	}
	fsi = fi;
	fso = fo;
	/*
	 * Validate the given file system size.
	 * Verify that its last block can actually be accessed.
	 */
	if (Oflag <= 1 && fssize > INT_MAX)
		errx(13, "preposterous size %lld, max is %d", fssize, INT_MAX);
	if (Oflag == 2 && fssize > MAXDISKSIZE)
		errx(13, "preposterous size %lld, max is %lld", fssize,
		    MAXDISKSIZE);

	wtfs(fssize - 1, sectorsize, (char *)&sblock);

	sblock.fs_postblformat = FS_DYNAMICPOSTBLFMT;
	sblock.fs_avgfilesize = avgfilesize;
	sblock.fs_avgfpdir = avgfilesperdir;

	/*
	 * Collect and verify the block and fragment sizes.
	 */
	if (!POWEROF2(bsize)) {
		errx(16, "block size must be a power of 2, not %d", bsize);
	}
	if (!POWEROF2(fsize)) {
		errx(17, "fragment size must be a power of 2, not %d",
		     fsize);
	}
	if (fsize < sectorsize) {
		errx(18, "fragment size %d is too small, minimum is %d",
		     fsize, sectorsize);
	}
	if (bsize < MINBSIZE) {
		errx(19, "block size %d is too small, minimum is %d",
		     bsize, MINBSIZE);
	}
	if (bsize > MAXBSIZE) {
		errx(19, "block size %d is too large, maximum is %d",
		     bsize, MAXBSIZE);
	}
	if (bsize < fsize) {
		errx(20, "block size (%d) cannot be smaller than fragment size (%d)",
		     bsize, fsize);
	}
	sblock.fs_bsize = bsize;
	sblock.fs_fsize = fsize;

	/*
	 * Calculate the superblock bitmasks and shifts.
	 */
	sblock.fs_bmask = ~(sblock.fs_bsize - 1);
	sblock.fs_fmask = ~(sblock.fs_fsize - 1);
	sblock.fs_qbmask = ~sblock.fs_bmask;
	sblock.fs_qfmask = ~sblock.fs_fmask;
	sblock.fs_bshift = ilog2(sblock.fs_bsize);
	sblock.fs_fshift = ilog2(sblock.fs_fsize);
	sblock.fs_frag = numfrags(&sblock, sblock.fs_bsize);
	if (sblock.fs_frag > MAXFRAG) {
		errx(21, "fragment size %d is too small, minimum with block "
		    "size %d is %d", sblock.fs_fsize, sblock.fs_bsize,
		    sblock.fs_bsize / MAXFRAG);
	}
	sblock.fs_fragshift = ilog2(sblock.fs_frag);
	sblock.fs_fsbtodb = ilog2(sblock.fs_fsize / sectorsize);
	sblock.fs_size = dbtofsb(&sblock, fssize);
	sblock.fs_nspf = sblock.fs_fsize / sectorsize;
	sblock.fs_maxcontig = 1;
	sblock.fs_nrpos = 1;
	sblock.fs_cpg = 1;

	/*
	 * Before the file system is fully initialized, mark it as invalid.
	 */
	sblock.fs_magic = FS_BAD_MAGIC;

	/*
	 * Set the remaining superblock fields.  Note that for FFS1, media
	 * geometry fields are set to fake values.  This is for compatibility
	 * with really ancient kernels that might still inspect these values.
	 */
	if (Oflag <= 1) {
		sblock.fs_sblockloc = SBLOCK_UFS1;
		sblock.fs_nindir = sblock.fs_bsize / sizeof(int32_t);
		sblock.fs_inopb = sblock.fs_bsize / sizeof(struct ufs1_dinode);
		if (Oflag == 0) {
			sblock.fs_maxsymlinklen = 0;
			sblock.fs_inodefmt = FS_42INODEFMT;
		} else {
			sblock.fs_maxsymlinklen = MAXSYMLINKLEN_UFS1;
			sblock.fs_inodefmt = FS_44INODEFMT;
		}
		sblock.fs_cgoffset = 0;
		sblock.fs_cgmask = 0xffffffff;
		sblock.fs_ffs1_size = sblock.fs_size;
		sblock.fs_rotdelay = 0;
		sblock.fs_rps = 60;
		sblock.fs_interleave = 1;
		sblock.fs_trackskew = 0;
		sblock.fs_cpc = 0;
	} else {
		sblock.fs_inodefmt = FS_44INODEFMT;
		sblock.fs_sblockloc = SBLOCK_UFS2;
		sblock.fs_nindir = sblock.fs_bsize / sizeof(int64_t);
		sblock.fs_inopb = sblock.fs_bsize / sizeof(struct ufs2_dinode);
		sblock.fs_maxsymlinklen = MAXSYMLINKLEN_UFS2;
	}
	sblock.fs_sblkno =
	    roundup(howmany(sblock.fs_sblockloc + SBLOCKSIZE, sblock.fs_fsize),
		sblock.fs_frag);
	sblock.fs_cblkno = (int32_t)(sblock.fs_sblkno +
	    roundup(howmany(SBSIZE, sblock.fs_fsize), sblock.fs_frag));
	sblock.fs_iblkno = sblock.fs_cblkno + sblock.fs_frag;
	sblock.fs_maxfilesize = sblock.fs_bsize * NDADDR - 1;
	for (sizepb = sblock.fs_bsize, i = 0; i < NIADDR; i++) {
		sizepb *= NINDIR(&sblock);
		sblock.fs_maxfilesize += sizepb;
	}
#ifdef notyet
	/*
	 * It is impossible to create a snapshot in case fs_maxfilesize is
	 * smaller than fssize.
	 */
	if (sblock.fs_maxfilesize < (u_quad_t)fssize)
		warnx("WARNING: You will be unable to create snapshots on this "
		    "file system. Correct by using a larger blocksize.");
#endif
	/*
	 * Calculate the number of blocks to put into each cylinder group. The
	 * first goal is to have at least enough data blocks in each cylinder
	 * group to meet the density requirement. Once this goal is achieved
	 * we try to expand to have at least mincylgrps cylinder groups. Once
	 * this goal is achieved, we pack as many blocks into each cylinder
	 * group map as will fit.
	 *
	 * We start by calculating the smallest number of blocks that we can
	 * put into each cylinder group. If this is too big, we reduce the
	 * density until it fits.
	 */
	origdensity = density;
	for (;;) {
		fragsperinode = MAX(numfrags(&sblock, density), 1);

		minfpg = fragsperinode * INOPB(&sblock);
		if (minfpg > sblock.fs_size)
			minfpg = sblock.fs_size;

		sblock.fs_ipg = INOPB(&sblock);
		sblock.fs_fpg = roundup(sblock.fs_iblkno +
		    sblock.fs_ipg / INOPF(&sblock), sblock.fs_frag);
		if (sblock.fs_fpg < minfpg)
			sblock.fs_fpg = minfpg;

		sblock.fs_ipg = roundup(howmany(sblock.fs_fpg, fragsperinode),
		    INOPB(&sblock));
		sblock.fs_fpg = roundup(sblock.fs_iblkno +
		    sblock.fs_ipg / INOPF(&sblock), sblock.fs_frag);
		if (sblock.fs_fpg < minfpg)
			sblock.fs_fpg = minfpg;

		sblock.fs_ipg = roundup(howmany(sblock.fs_fpg, fragsperinode),
		    INOPB(&sblock));

		if (CGSIZE(&sblock) < (unsigned long)sblock.fs_bsize)
			break;

		density -= sblock.fs_fsize;
	}
	if (density != origdensity)
		warnx("density reduced from %d to %d bytes per inode",
		    origdensity, density);

	/*
	 * Use a lower value for mincylgrps if the user specified a large
	 * number of blocks per cylinder group.  This is needed for, e.g. the
	 * install media which needs to pack 2 files very tightly.
	 */
	mincylgrps = MINCYLGRPS;
	if (maxfrgspercg != INT_MAX) {
		i = sblock.fs_size / maxfrgspercg;
		if (i < MINCYLGRPS)
			mincylgrps = i <= 0 ? 1 : i;
	}

	/*
	 * Start packing more blocks into the cylinder group until it cannot
	 * grow any larger, the number of cylinder groups drops below
	 * mincylgrps, or we reach the requested size.
	 */
	for (;;) {
		sblock.fs_fpg += sblock.fs_frag;
		sblock.fs_ipg = roundup(howmany(sblock.fs_fpg, fragsperinode),
		    INOPB(&sblock));

		if (sblock.fs_fpg > maxfrgspercg ||
		    sblock.fs_size / sblock.fs_fpg < mincylgrps ||
		    CGSIZE(&sblock) > (unsigned long)sblock.fs_bsize)
			break;
	}
	sblock.fs_fpg -= sblock.fs_frag;
	sblock.fs_ipg = roundup(howmany(sblock.fs_fpg, fragsperinode),
	    INOPB(&sblock));
	if (sblock.fs_fpg > maxfrgspercg)
		warnx("can't honour -c: minimum is %d", sblock.fs_fpg);

	/*
	 * Check to be sure that the last cylinder group has enough blocks to
	 * be viable. If it is too small, reduce the number of blocks per
	 * cylinder group which will have the effect of moving more blocks into
	 * the last cylinder group.
	 */
	optimalfpg = sblock.fs_fpg;
	for (;;) {
		sblock.fs_ncg = howmany(sblock.fs_size, sblock.fs_fpg);
		lastminfpg = roundup(sblock.fs_iblkno +
		    sblock.fs_ipg / INOPF(&sblock), sblock.fs_frag);
		if (sblock.fs_size < lastminfpg)
			errx(28, "file system size %jd < minimum size of %d",
			    (intmax_t)sblock.fs_size, lastminfpg);

		if (sblock.fs_size % sblock.fs_fpg >= lastminfpg ||
		    sblock.fs_size % sblock.fs_fpg == 0)
			break;

		sblock.fs_fpg -= sblock.fs_frag;
		sblock.fs_ipg = roundup(howmany(sblock.fs_fpg, fragsperinode),
		    INOPB(&sblock));
	}

	if (optimalfpg != sblock.fs_fpg)
		warnx("reduced number of fragments per cylinder group from %d"
		    " to %d to enlarge last cylinder group", optimalfpg,
		    sblock.fs_fpg);

	/*
	 * Back to filling superblock fields.
	 */
	if (Oflag <= 1) {
		sblock.fs_spc = sblock.fs_fpg * sblock.fs_nspf;
		sblock.fs_nsect = sblock.fs_spc;
		sblock.fs_npsect = sblock.fs_spc;
		sblock.fs_ncyl = sblock.fs_ncg;
	}
	sblock.fs_cgsize = fragroundup(&sblock, CGSIZE(&sblock));
	sblock.fs_dblkno = sblock.fs_iblkno + sblock.fs_ipg / INOPF(&sblock);
	sblock.fs_csaddr = cgdmin(&sblock, 0);
	sblock.fs_cssize =
	    fragroundup(&sblock, sblock.fs_ncg * sizeof(struct csum));

	fscs = (struct csum *)calloc(1, sblock.fs_cssize);
	if (fscs == NULL)
		errx(31, "calloc failed");

	sblock.fs_sbsize = fragroundup(&sblock, sizeof(struct fs));
	if (sblock.fs_sbsize > SBLOCKSIZE)
		sblock.fs_sbsize = SBLOCKSIZE;

	sblock.fs_minfree = minfree;
	sblock.fs_maxbpg = maxbpg;
	sblock.fs_optim = opt;
	sblock.fs_cgrotor = 0;
	sblock.fs_pendingblocks = 0;
	sblock.fs_pendinginodes = 0;
	sblock.fs_fmod = 0;
	sblock.fs_ronly = 0;
	sblock.fs_state = 0;
	sblock.fs_clean = 1;
	sblock.fs_id[0] = (u_int32_t)utime;
	sblock.fs_id[1] = (u_int32_t)arc4random();
	sblock.fs_fsmnt[0] = '\0';

	csfrags = howmany(sblock.fs_cssize, sblock.fs_fsize);
	sblock.fs_dsize = sblock.fs_size - sblock.fs_sblkno -
	    sblock.fs_ncg * (sblock.fs_dblkno - sblock.fs_sblkno);

	sblock.fs_cstotal.cs_nbfree = fragstoblks(&sblock, sblock.fs_dsize) -
	    howmany(csfrags, sblock.fs_frag);
	sblock.fs_cstotal.cs_nffree = fragnum(&sblock, sblock.fs_size) +
	    (fragnum(&sblock, csfrags) > 0 ?
	    sblock.fs_frag - fragnum(&sblock, csfrags) : 0);
	sblock.fs_cstotal.cs_nifree = sblock.fs_ncg * sblock.fs_ipg - ROOTINO;
	sblock.fs_cstotal.cs_ndir = 0;

	sblock.fs_dsize -= csfrags;
	sblock.fs_time = utime;

	if (Oflag <= 1) {
		sblock.fs_ffs1_time = sblock.fs_time;
		sblock.fs_ffs1_dsize = sblock.fs_dsize;
		sblock.fs_ffs1_csaddr = sblock.fs_csaddr;
		sblock.fs_ffs1_cstotal.cs_ndir = sblock.fs_cstotal.cs_ndir;
		sblock.fs_ffs1_cstotal.cs_nbfree = sblock.fs_cstotal.cs_nbfree;
		sblock.fs_ffs1_cstotal.cs_nifree = sblock.fs_cstotal.cs_nifree;
		sblock.fs_ffs1_cstotal.cs_nffree = sblock.fs_cstotal.cs_nffree;
	}

	/*
	 * Dump out summary information about file system.
	 */
	if (!mfs) {
#define B2MBFACTOR (1 / (1024.0 * 1024.0))
		printf("%s: %.1fMB in %jd sectors of %d bytes\n", fsys,
		    (float)sblock.fs_size * sblock.fs_fsize * B2MBFACTOR,
		    (intmax_t)fsbtodb(&sblock, sblock.fs_size), sectorsize);
		printf("%d cylinder groups of %.2fMB, %d blocks, %d"
		    " inodes each\n", sblock.fs_ncg,
		    (float)sblock.fs_fpg * sblock.fs_fsize * B2MBFACTOR,
		    sblock.fs_fpg / sblock.fs_frag, sblock.fs_ipg);
#undef B2MBFACTOR
	}

	/*
	 * Wipe out old FFS1 superblock if necessary.
	 */
	if (Oflag >= 2) {
		union fs_u *fsun1;
		struct fs *fs1;

		fsun1 = calloc(1, sizeof(union fs_u));
		if (fsun1 == NULL)
			err(39, "calloc");
		fs1 = &fsun1->fs;
		rdfs(SBLOCK_UFS1 / sectorsize, SBSIZE, (char *)fs1);
		if (fs1->fs_magic == FS_UFS1_MAGIC) {
			fs1->fs_magic = FS_BAD_MAGIC;
			wtfs(SBLOCK_UFS1 / sectorsize, SBSIZE, (char *)fs1);
		}
		free(fsun1);
	}

	wtfs((int)sblock.fs_sblockloc / sectorsize, SBSIZE, (char *)&sblock);
	sblock.fs_magic = (Oflag <= 1) ? FS_UFS1_MAGIC : FS_UFS2_MAGIC;

	/*
	 * Now build the cylinders group blocks and
	 * then print out indices of cylinder groups.
	 */
	if (!quiet)
		printf("super-block backups (for fsck -b #) at:\n");
#ifndef STANDALONE
	else if (!mfs && isatty(STDIN_FILENO)) {
		signal(SIGINFO, siginfo);
		cur_fsys = fsys;
	}
#endif
	i = 0;
	width = charsperline();
	/*
	* Allocate space for superblock, cylinder group map, and two sets of
	* inode blocks.
	*/
	if (sblock.fs_bsize < SBLOCKSIZE)
		iobufsize = SBLOCKSIZE + 3 * sblock.fs_bsize;
	else
		iobufsize = 4 * sblock.fs_bsize;
	if ((iobuf = malloc(iobufsize)) == 0)
		errx(38, "cannot allocate I/O buffer");
	bzero(iobuf, iobufsize);
	/*
	 * Make a copy of the superblock into the buffer that we will be
	 * writing out in each cylinder group.
	 */
	bcopy((char *)&sblock, iobuf, SBLOCKSIZE);
	for (cylno = 0; cylno < sblock.fs_ncg; cylno++) {
		cur_cylno = (sig_atomic_t)cylno;
		initcg(cylno, utime);
		if (quiet)
			continue;
		j = snprintf(tmpbuf, sizeof tmpbuf, " %lld,",
		    fsbtodb(&sblock, cgsblock(&sblock, cylno)));
		if (j >= sizeof tmpbuf)
			j = sizeof tmpbuf - 1;
		if (j == -1 || i+j >= width) {
			printf("\n");
			i = 0;
		}
		i += j;
		printf("%s", tmpbuf);
		fflush(stdout);
	}
	if (!quiet)
		printf("\n");
	if (Nflag && !mfs)
		exit(0);
	/*
	 * Now construct the initial file system, then write out the superblock.
	 */
	if (Oflag <= 1) {
		if (fsinit1(utime, mfsmode, mfsuid, mfsgid))
			errx(32, "fsinit1 failed");
		sblock.fs_ffs1_cstotal.cs_ndir = sblock.fs_cstotal.cs_ndir;
		sblock.fs_ffs1_cstotal.cs_nbfree = sblock.fs_cstotal.cs_nbfree;
		sblock.fs_ffs1_cstotal.cs_nifree = sblock.fs_cstotal.cs_nifree;
		sblock.fs_ffs1_cstotal.cs_nffree = sblock.fs_cstotal.cs_nffree;
	} else {
		if (fsinit2(utime))
			errx(32, "fsinit2 failed");
	}

	wtfs((int)sblock.fs_sblockloc / sectorsize, SBSIZE, (char *)&sblock);

	for (i = 0; i < sblock.fs_cssize; i += sblock.fs_bsize)
		wtfs(fsbtodb(&sblock, sblock.fs_csaddr + numfrags(&sblock, i)),
		    sblock.fs_cssize - i < sblock.fs_bsize ?
		    sblock.fs_cssize - i : sblock.fs_bsize,
		    ((char *)fscs) + i);

	/*
	 * Update information about this partion in pack label, to that it may
	 * be updated on disk.
	 */
	pp->p_fstype = FS_BSDFFS;
	pp->p_fragblock =
	    DISKLABELV1_FFS_FRAGBLOCK(sblock.fs_fsize, sblock.fs_frag);
	pp->p_cpg = sblock.fs_cpg;
}
Beispiel #12
0
/*
 * Here we dump a list of all blocks allocated by this inode. We follow
 * all indirect blocks.
 */
void
dump_whole_inode(ino_t inode, int fsi, int level)
{
	struct ufs1_dinode	*ino;
	int	rb;
	unsigned int	ind2ctr, ind3ctr;
	ufs_daddr_t	*ind2ptr, *ind3ptr;
	char	comment[80];
	
	DBG_ENTER;

	/*
	 * Read the inode from disk/cache.
	 */
	ino=ginode(inode, fsi);

	if(ino->di_nlink==0) {
		DBG_LEAVE;
		return;	/* inode not in use */
	}

	/*
	 * Dump the main inode structure.
	 */
	snprintf(comment, sizeof(comment), "Inode 0x%08jx", (uintmax_t)inode);
	if (level & 0x100) {
		DBG_DUMP_INO(&sblock,
		    comment,
		    ino);
	}

	if (!(level & 0x200)) {
		DBG_LEAVE;
		return;
	}

	/*
	 * Ok, now prepare for dumping all direct and indirect pointers.
	 */
	rb=howmany(ino->di_size, sblock.fs_bsize)-UFS_NDADDR;
	if(rb>0) {
		/*
		 * Dump single indirect block.
		 */
		rdfs(fsbtodb(&sblock, ino->di_ib[0]), (size_t)sblock.fs_bsize,
		    &i1blk, fsi);
		snprintf(comment, sizeof(comment), "Inode 0x%08jx: indirect 0",
		    (uintmax_t)inode);
		DBG_DUMP_IBLK(&sblock,
		    comment,
		    i1blk,
		    (size_t)rb);
		rb-=howmany(sblock.fs_bsize, sizeof(ufs_daddr_t));
	}
	if(rb>0) {
		/*
		 * Dump double indirect blocks.
		 */
		rdfs(fsbtodb(&sblock, ino->di_ib[1]), (size_t)sblock.fs_bsize,
		    &i2blk, fsi);
		snprintf(comment, sizeof(comment), "Inode 0x%08jx: indirect 1",
		    (uintmax_t)inode);
		DBG_DUMP_IBLK(&sblock,
		    comment,
		    i2blk,
		    howmany(rb, howmany(sblock.fs_bsize, sizeof(ufs_daddr_t))));
		for(ind2ctr=0; ((ind2ctr < howmany(sblock.fs_bsize,
		    sizeof(ufs_daddr_t)))&&(rb>0)); ind2ctr++) {
			ind2ptr=&((ufs_daddr_t *)(void *)&i2blk)[ind2ctr];

			rdfs(fsbtodb(&sblock, *ind2ptr),
			    (size_t)sblock.fs_bsize, &i1blk, fsi);
			snprintf(comment, sizeof(comment),
			    "Inode 0x%08jx: indirect 1->%d", (uintmax_t)inode,
			    ind2ctr);
			DBG_DUMP_IBLK(&sblock,
			    comment,
			    i1blk,
			    (size_t)rb);
			rb-=howmany(sblock.fs_bsize, sizeof(ufs_daddr_t));
		}
	}
	if(rb>0) {
		/*
		 * Dump triple indirect blocks.
		 */
		rdfs(fsbtodb(&sblock, ino->di_ib[2]), (size_t)sblock.fs_bsize,
		    &i3blk, fsi);
		snprintf(comment, sizeof(comment), "Inode 0x%08jx: indirect 2",
		    (uintmax_t)inode);
#define SQUARE(a) ((a)*(a))
		DBG_DUMP_IBLK(&sblock,
		    comment,
		    i3blk,
		    howmany(rb,
		      SQUARE(howmany(sblock.fs_bsize, sizeof(ufs_daddr_t)))));
#undef SQUARE
		for(ind3ctr=0; ((ind3ctr < howmany(sblock.fs_bsize,
		    sizeof(ufs_daddr_t)))&&(rb>0)); ind3ctr ++) {
			ind3ptr=&((ufs_daddr_t *)(void *)&i3blk)[ind3ctr];

			rdfs(fsbtodb(&sblock, *ind3ptr),
			    (size_t)sblock.fs_bsize, &i2blk, fsi);
			snprintf(comment, sizeof(comment),
			    "Inode 0x%08jx: indirect 2->%d", (uintmax_t)inode,
			    ind3ctr);
			DBG_DUMP_IBLK(&sblock,
			    comment,
			    i2blk,
			    howmany(rb,
			      howmany(sblock.fs_bsize, sizeof(ufs_daddr_t))));
			for(ind2ctr=0; ((ind2ctr < howmany(sblock.fs_bsize,
			    sizeof(ufs_daddr_t)))&&(rb>0)); ind2ctr ++) {
				ind2ptr=&((ufs_daddr_t *)(void *)&i2blk)
				    [ind2ctr];
				rdfs(fsbtodb(&sblock, *ind2ptr),
				    (size_t)sblock.fs_bsize, &i1blk, fsi);
				snprintf(comment, sizeof(comment),
				    "Inode 0x%08jx: indirect 2->%d->%d",
				    (uintmax_t)inode, ind3ctr, ind3ctr);
				DBG_DUMP_IBLK(&sblock,
				    comment,
				    i1blk,
				    (size_t)rb);
				rb-=howmany(sblock.fs_bsize,
				    sizeof(ufs_daddr_t));
			}
		}
	}

	DBG_LEAVE;
	return;
}
Beispiel #13
0
/*
 * ffsinfo(8) is a tool to dump all metadata of a filesystem. It helps to find
 * errors is the filesystem much easier. You can run ffsinfo before and  after
 * an  fsck(8),  and compare the two ascii dumps easy with diff, and  you  see
 * directly where the problem is. You can control how much detail you want  to
 * see  with some command line arguments. You can also easy check  the  status
 * of  a filesystem, like is there is enough space for growing  a  filesystem,
 * or  how  many active snapshots do we have. It provides much  more  detailed
 * information  then dumpfs. Snapshots, as they are very new, are  not  really
 * supported.  They  are just mentioned currently, but it is  planned  to  run
 * also over active snapshots, to even get that output.
 */
int
main(int argc, char **argv)
{
	char	*device, *special;
	char	ch;
	size_t	len;
	struct stat	st;
	struct partinfo pinfo;
	int	fsi;
	struct csum	*dbg_csp;
	int	dbg_csc;
	char	dbg_line[80];
	int	cylno,i;
	int	cfg_cg, cfg_in, cfg_lv;
	int	cg_start, cg_stop;
	ino_t	in;
	char	*out_file = NULL;
	int	Lflag=0;

	DBG_ENTER;

	cfg_lv=0xff;
	cfg_in=-2;
	cfg_cg=-2;

	while ((ch=getopt(argc, argv, "Lg:i:l:o:")) != -1) {
		switch(ch) {
		case 'L':
			Lflag=1;
			break;
		case 'g':
			cfg_cg=atol(optarg);
			if(cfg_cg < -1) {
				usage();
			}
			break;
		case 'i':
			cfg_in=atol(optarg);
			if(cfg_in < 0) {
				usage();
			}
			break; 
		case 'l':
			cfg_lv=atol(optarg);
			if(cfg_lv < 0x1||cfg_lv > 0x3ff) {
				usage();
			}
			break;
		case 'o':
			if (out_file)
				free(out_file);
			out_file = strdup(optarg);
			break;
		case '?':
			/* FALLTHROUGH */
		default:
			usage();
		}
	}
	argc -= optind;
	argv += optind;

	if(argc != 1) {
		usage();
	}
	device=*argv;
	
	/*
	 * Now we try to guess the (raw)device name.
	 */
	if (0 == strrchr(device, '/') && (stat(device, &st) == -1)) {
		/*
		 * No path prefix was given, so try in that order:
		 *     /dev/r%s
		 *     /dev/%s
		 *     /dev/vinum/r%s
		 *     /dev/vinum/%s.
		 * 
		 * FreeBSD now doesn't distinguish between raw and  block
		 * devices any longer, but it should still work this way.
		 */
		len=strlen(device)+strlen(_PATH_DEV)+2+strlen("vinum/");
		special=(char *)malloc(len);
		if(special == NULL) {
			errx(1, "malloc failed");
		}
		snprintf(special, len, "%sr%s", _PATH_DEV, device);
		if (stat(special, &st) == -1) {
			snprintf(special, len, "%s%s", _PATH_DEV, device);
			if (stat(special, &st) == -1) {
				snprintf(special, len, "%svinum/r%s",
				    _PATH_DEV, device);
				if (stat(special, &st) == -1) {
					/*
					 * For now this is the 'last resort'.
					 */
					snprintf(special, len, "%svinum/%s",
					    _PATH_DEV, device);
				}
			}
		}
		device = special;
	}

	/*
	 * Open our device for reading.
	 */
	fsi = open(device, O_RDONLY);
	if (fsi < 0) {
		err(1, "%s", device);
	}

	stat(device, &st);
	
	if(S_ISREG(st.st_mode)) { /* label check not supported for files */
		Lflag=1;
	}

	if(!Lflag) {
		/*
		 * Try  to read a label and gess the slice if not  specified.
		 * This code should guess the right thing and avaid to bother
		 * the user user with the task of specifying the option -v on
		 * vinum volumes.
		 */
		if (ioctl(fsi, DIOCGPART, &pinfo) < 0) {
			pinfo.media_size = st.st_size;
			pinfo.media_blksize = DEV_BSIZE;
			pinfo.media_blocks = pinfo.media_size / DEV_BSIZE;
		}
	
		/*
		 * Check if that partition looks suited for dumping.
		 */
		if (pinfo.media_size == 0) {
			errx(1, "partition is unavailable");
		}
	}

	/*
	 * Read the current superblock.
	 */
	rdfs((daddr_t)(SBOFF/DEV_BSIZE), (size_t)SBSIZE, &sblock, fsi);
	if (sblock.fs_magic != FS_MAGIC) {
		errx(1, "superblock not recognized");
	}

	DBG_OPEN(out_file); /* already here we need a superblock */

	if(cfg_lv & 0x001) {
		DBG_DUMP_FS(&sblock,
		    "primary sblock");
	}

	/*
	 * Determine here what cylinder groups to dump.
	 */
	if(cfg_cg==-2) {
		cg_start=0;
		cg_stop=sblock.fs_ncg;
	} else if (cfg_cg==-1) {
		cg_start=sblock.fs_ncg-1;
		cg_stop=sblock.fs_ncg;
	} else if (cfg_cg<sblock.fs_ncg) {
		cg_start=cfg_cg;
		cg_stop=cfg_cg+1;
	} else {
		cg_start=sblock.fs_ncg;
		cg_stop=sblock.fs_ncg;
	}

	if (cfg_lv & 0x004) {
		fscs = (struct csum *)calloc((size_t)1,
		    (size_t)sblock.fs_cssize);
		if(fscs == NULL) {
			errx(1, "calloc failed");
		}

		/*
		 * Get the cylinder summary into the memory ...
		 */
		for (i = 0; i < sblock.fs_cssize; i += sblock.fs_bsize) {
			rdfs(fsbtodb(&sblock, sblock.fs_csaddr +
			    numfrags(&sblock, i)), (size_t)(sblock.fs_cssize-i<
			    sblock.fs_bsize ? sblock.fs_cssize - i :
			    sblock.fs_bsize), (void *)(((char *)fscs)+i), fsi);
		}

		dbg_csp=fscs;
		/*
		 * ... and dump it.
		 */
		for(dbg_csc=0; dbg_csc<sblock.fs_ncg; dbg_csc++) {
			snprintf(dbg_line, sizeof(dbg_line),
			    "%d. csum in fscs", dbg_csc);
			DBG_DUMP_CSUM(&sblock,
			    dbg_line,
			    dbg_csp++);
		}
	}

	/*
	 * For each requested cylinder group ...
	 */
	for(cylno=cg_start; cylno<cg_stop; cylno++) {
		snprintf(dbg_line, sizeof(dbg_line), "cgr %d", cylno);
		if(cfg_lv & 0x002) {
			/*
			 * ... dump the superblock copies ...
			 */
			rdfs(fsbtodb(&sblock, cgsblock(&sblock, cylno)),
			    (size_t)SBSIZE, &osblock, fsi);
			DBG_DUMP_FS(&osblock,
			    dbg_line);
		}
		/*
		 * ... read the cylinder group and dump whatever was requested.
		 */
		rdfs(fsbtodb(&sblock, cgtod(&sblock, cylno)),
		    (size_t)sblock.fs_cgsize, &acg, fsi);
		if(cfg_lv & 0x008) {
			DBG_DUMP_CG(&sblock,
			    dbg_line,
			    &acg);
		}
		if(cfg_lv & 0x010) {
			DBG_DUMP_INMAP(&sblock,
			    dbg_line,
			    &acg);
		}
		if(cfg_lv & 0x020) {
			DBG_DUMP_FRMAP(&sblock,
			    dbg_line,
			    &acg);
		}
		if(cfg_lv & 0x040) {
			DBG_DUMP_CLMAP(&sblock,
			    dbg_line,
			    &acg);
			DBG_DUMP_CLSUM(&sblock,
			    dbg_line,
			    &acg);
		}
		if(cfg_lv & 0x080) {
			DBG_DUMP_SPTBL(&sblock,
			    dbg_line,
			    &acg);
		}
	}
	/*
	 * Dump the requested inode(s).
	 */
	if(cfg_in != -2) {
		dump_whole_inode((ino_t)cfg_in, fsi, cfg_lv);
	} else {
		for(in=cg_start*sblock.fs_ipg; in<(ino_t)cg_stop*sblock.fs_ipg;
		    in++) {
			dump_whole_inode(in, fsi, cfg_lv);
		}
	}

	DBG_CLOSE;

	close(fsi);

	DBG_LEAVE;
	return 0;
}
// construct the prdf profile
static PyObject *func_construct_prdf(PyObject *self, PyObject *args)
{
	// local variables
	double cube_length;
	int nx, ny, nz;
	double x0, y0, z0;
	double prdf_spacing;
	int prdf_n;
	double cutoff_distance;
	size_t i;
	PyObject * item;

	// parse the argument list
    PyObject * py_solute_atom_types, * py_solvent_atom_types;
	PyObject * py_solute_atom_surf_mask;
    PyObject * py_solute_atom_coors, * py_solvent_atom_coors;
    if (!PyArg_ParseTuple(args, "O!O!O!O!O!ddddiiidid", &PyList_Type, &py_solute_atom_types, &PyArray_Type, &py_solute_atom_coors, &PyList_Type, &py_solvent_atom_types, &PyArray_Type, &py_solvent_atom_coors, &PyArray_Type, &py_solute_atom_surf_mask, &x0, &y0, &z0, &cube_length, &nx, &ny, &nz, &prdf_spacing, &prdf_n, &cutoff_distance))
		return NULL;

	// define types
	typedef Atom::SoluteAtom::SoluteAtomType solute_atom_type_t;
	typedef Atom::SolventAtom::SolventAtomType solvent_atom_type_t;

	// get the number of frames, and solute/solvent atoms
    PyArrayObject * pyArray_solute_atom_coors = (PyArrayObject*)PyArray_ContiguousFromObject(py_solute_atom_coors,PyArray_DOUBLE, 2,2);
    PyArrayObject * pyArray_solvent_atom_coors = (PyArrayObject*)PyArray_ContiguousFromObject(py_solvent_atom_coors,PyArray_DOUBLE, 3,3);
	const size_t tot_frames=pyArray_solvent_atom_coors->dimensions[0];
	const size_t n_solute_atoms = PyList_Size(py_solute_atom_types);
	const size_t n_solvent_atoms = PyList_Size(py_solvent_atom_types);
std::cout<<__LINE__<<std::endl;

	// get the solute atom surface mask
    PyArrayObject * pyArray_solute_atom_surf_mask = (PyArrayObject*)PyArray_ContiguousFromObject(py_solute_atom_surf_mask,PyArray_INT, 1,1);
std::cout<<__LINE__<<std::endl;

	// convert python types to C types
	solute_atom_type_t * solute_atom_types = new solute_atom_type_t[n_solute_atoms];
	for (i=0; i<n_solute_atoms; i++)
	{
		item  = PyList_GetItem(py_solute_atom_types, i);
		if (!PyString_Check(item)) prdf::utils::Error("solute atom type should be a string!");
		solute_atom_types[i] = PyString_AsString(item);
	}
	solvent_atom_type_t * solvent_atom_types = new solvent_atom_type_t[n_solvent_atoms];
	for (i=0; i<n_solvent_atoms; i++)
	{
		item  = PyList_GetItem(py_solvent_atom_types, i);
		if (!PyString_Check(item)) prdf::utils::Error("solvent atom type should be a string!");
		solvent_atom_types[i] = PyString_AsString(item);
	}
	double * solute_atom_coors = (double*)(pyArray_solute_atom_coors->data);
	double * solvent_atom_coors = (double*)(pyArray_solvent_atom_coors->data);
	int * solute_atom_surf_mask = (int*)(pyArray_solute_atom_surf_mask->data);
std::cout<<__LINE__<<std::endl;
	/*
	std::cout<<"c0: "<<x0<<" "<<y0<<" "<<z0<<std::endl;
	std::cout<<"nx/y/z: "<<nx<<" "<<ny<<" "<<nz<<std::endl;
	std::cout<<"cube_l: "<<cube_length<<std::endl;
	std::cout<<"prfd_n/spacing: "<<prdf_n<<" "<<prdf_spacing<<std::endl;
	std::cout<<"n_slute: "<<n_solute_atoms<<" n_solv: "<<n_solvent_atoms<<std::endl;
	std::cout<<"c0 solute: "<<solute_atom_coors[0]<<" "<<solute_atom_coors[1]<<" "<<solute_atom_coors[2]<<std::endl;
	std::cout<<"c1 solute: "<<solute_atom_coors[3]<<" "<<solute_atom_coors[4]<<" "<<solute_atom_coors[5]<<std::endl;
	std::cout<<"c0 solvent: "<<solvent_atom_coors[0]<<" "<<solvent_atom_coors[1]<<" "<<solvent_atom_coors[2]<<std::endl;
	std::cout<<"c1 solvent: "<<solvent_atom_coors[3]<<" "<<solvent_atom_coors[4]<<" "<<solvent_atom_coors[5]<<std::endl;
	for (i=0; i<n_solute_atoms; i++) std::cout<<solute_atom_surf_mask[i]<<std::endl;
	*/

	// box parameters
	Coor coor_box_origin(x0, y0, z0);
	// set up the box
	Box box(coor_box_origin, nx, ny, nz, cube_length);
std::cout<<__LINE__<<std::endl;

	// prdf parameters
	// set up prdf
	pRDF rdfs(prdf_n, prdf_spacing);
std::cout<<__LINE__<<std::endl;

	// set up the cubes in box
	box.setupCube(n_solute_atoms, solute_atom_types, solute_atom_coors, solute_atom_surf_mask, cutoff_distance); // set up the _p_cube_type_distance from the passed solute atom set
	// print out the types and distances values of all the not-null cubes for debugging
	box.fprintfTypeDistancePDB("box_type_distance.pdb");
std::cout<<__LINE__<<std::endl;

	// accumulate the solvent density into cubes
	for (size_t frame = 0; frame<tot_frames; ++frame)
	{
		// accumulate the solvent density into cubes
		box.accumulateCubeDensity(n_solvent_atoms, solvent_atom_types, solvent_atom_coors+frame*n_solvent_atoms*3);
	}
std::cout<<__LINE__<<std::endl;

	// finally update the pRDF based on the box
	rdfs.update(box);
std::cout<<__LINE__<<std::endl;

	// output pRDF
	std::ofstream fout("pRDF.txt");
	rdfs.print(fout,box,tot_frames);
	fout.close();
std::cout<<__LINE__<<std::endl;

	// clean up
	delete [] solute_atom_types;
	delete [] solvent_atom_types;
std::cout<<__LINE__<<std::endl;

	// return
	Py_INCREF(Py_None);
std::cout<<__LINE__<<std::endl;
	return Py_None;
}
/// predict the prdf profile
static PyObject *func_predict_prdf(PyObject *self, PyObject *args)
{
	// local variables
	double cube_length;
	int nx, ny, nz;
	double x0, y0, z0;
	double cutoff_distance;
	size_t i;
	PyObject * item;

	// parse the argument list
    PyObject * py_solute_atom_types;
	PyObject * py_solute_atom_surf_mask;
    PyObject * py_solute_atom_coors;
    if (!PyArg_ParseTuple(args, "O!O!O!ddddiiid", &PyList_Type, &py_solute_atom_types, &PyArray_Type, &py_solute_atom_coors, &PyArray_Type, &py_solute_atom_surf_mask, &x0, &y0, &z0, &cube_length, &nx, &ny, &nz, &cutoff_distance))
		return NULL;

	// define types
	typedef Atom::SoluteAtom::SoluteAtomType solute_atom_type_t;
	typedef Atom::SolventAtom::SolventAtomType solvent_atom_type_t;

	// get the number of frames, and solute/solvent atoms
    PyArrayObject * pyArray_solute_atom_coors = (PyArrayObject*)PyArray_ContiguousFromObject(py_solute_atom_coors,PyArray_DOUBLE, 2,2);
	const size_t n_solute_atoms = PyList_Size(py_solute_atom_types);

	// get the solute atom surface mask
    PyArrayObject * pyArray_solute_atom_surf_mask = (PyArrayObject*)PyArray_ContiguousFromObject(py_solute_atom_surf_mask,PyArray_INT, 1,1);

	// convert python types to C types
	solute_atom_type_t * solute_atom_types = new solute_atom_type_t[n_solute_atoms];
	for (i=0; i<n_solute_atoms; i++)
	{
		item  = PyList_GetItem(py_solute_atom_types, i);
		if (!PyString_Check(item)) prdf::utils::Error("solute atom type should be a string!");
		solute_atom_types[i] = PyString_AsString(item);
	}
	double * solute_atom_coors = (double*)(pyArray_solute_atom_coors->data);
	int * solute_atom_surf_mask = (int*)(pyArray_solute_atom_surf_mask->data);

	// box parameters
	Coor coor_box_origin(x0, y0, z0);
	// set up the box
	Box box(coor_box_origin, nx, ny, nz, cube_length);

	// instantiate pRDF from the external file
	pRDF rdfs("pRDF.txt");

	// set up the cubes in box
	box.setupCube(n_solute_atoms, solute_atom_types, solute_atom_coors, solute_atom_surf_mask, cutoff_distance); // set up the _p_cube_type_distance from the passed solute atom set
	// print out the types and distances values of all the not-null cubes for debugging
	box.fprintfTypeDistancePDB("box_type_distance.pdb");

	// predict the solvent density in cubes
	box.predictCubeDensity(rdfs, cutoff_distance);

	// output box
	box.fprintfTypeDensityPDB("box_type_density.pdb");

	// clean up
	delete [] solute_atom_types;

	// return
	Py_INCREF(Py_None);
	return Py_None;
}
Beispiel #16
0
int main() {
    timestamp = 0;
    memset(visited, -1, sizeof(visited));
    int n, m, q;
    scanf("%d%d%d", &n, &m, &q);
    for (int i = 0; i < n; ++ i) {
        scanf("%d", weight + i);
    }
    for (int i = 0; i < m; ++ i) {
        int a, b;
        scanf("%d%d", &a, &b);
        a --;
        b --;
        graph[a].push_back(b);
        rgraph[b].push_back(a);
    }
    memset(match_x, -1, sizeof(match_x));
    memset(match_y, -1, sizeof(match_y));
    int sum = 0;
    {
        std::vector<int> order(n);
        std::iota(ALL(order), 0);
        std::sort(ALL(order), by_weight);
        memset(match_x, -1, sizeof(match_x));
        memset(match_y, -1, sizeof(match_y));
        timestamp ++;
        for (int v : order) {
            if (weight[v] < 0) {
                break;
            }
            if (find(v)) {
                sum += weight[v];
                timestamp ++;
            }
        }
    }
    while (q --) {
        int u, w;
        scanf("%d%d", &u, &w);
        u --;
        timestamp ++;
        do {
            if (match_x[u] == -1) {
                weight[u] = w;
                if (w < 0) {
                    continue;
                }
                if (find(u)) {
                    sum += weight[u];
                } else {
                    timestamp ++;
                    dfs(u);
                    int best = u;
                    for (int v = 0; v < n; ++ v) {
                        if (visited[v] == timestamp && weight[v] < weight[best]) {
                            best = v;
                        }
                    }
                    if (best != u) {
                        match_x[best] = -1;
                    }
                    for (int p = best; p != u; p = parent[p]) {
                        match_y[via[p]] = parent[p];
                        match_x[parent[p]] = via[p];
                    }
                    sum += weight[u] - weight[best];
                }
            } else {
                sum += w - weight[u];
                weight[u] = w;
                rdfs(u);
                int best = u;
                for (int v = 0; v < n; ++ v) {
                    if (visited[v] == timestamp && match_x[v] == -1 && weight[v] > weight[best]) {
                        best = v;
                    }
                }
                if (weight[best] <= 0) {
                    sum -= weight[u];
                    match_y[match_x[u]] = -1;
                    match_x[u] = -1;
                } else {
                    for (int p = best; p != u; p = parent[p]) {
                        match_x[p] = via[p];
                        match_y[via[p]] = p;
                    }
                    if (best != u) {
                        match_x[u] = -1;
                    }
                    sum += weight[best] - weight[u];
                }
            }
        } while (false);
        printf("%d\n", sum);
    }
    return 0;
}
Beispiel #17
0
/* write the memory-inode out to the inode-block */
void iput(struct inode *ip, int *aibc, s4_daddr *ib)
{
        struct s4_dinode *dp;
        s4_daddr  d;
        int       i,j,k;
        s4_daddr  ib2[NIDIR];	/* a double indirect block */

        filsys->s_tinode--;
        d = itod(ip->i_number);
        if(d >= filsys->s_isize) {
                if(error == 0)
                        printf("ilist too small\n");
                error = 1;
                return;
        }
     
        /* get the existing disk inode block to modify */
        rdfs(d, buf, s4b_ino );
        dp = (struct s4_dinode *)buf;
     
        /* skip to the right entry */
        dp += itoo(ip->i_number);

        /* convert memory to disk format in buffer */
        dp->di_mode  = ip->i_ftype | ip->i_mode;
        dp->di_nlink = ip->i_nlink;
        dp->di_uid   = ip->i_uid;
        dp->di_gid   = ip->i_gid;
        dp->di_size  = ip->i_size;
        dp->di_atime = utime;
        dp->di_mtime = utime;
        dp->di_ctime = utime;

        switch(ip->i_ftype) {

        case S_IFDIR:
        case S_IFREG:
     
                /* handle direct pointers */
                for(i=0; i<*aibc && i<LADDR; i++) {
                        ip->i_faddr[i] = ib[i];
                        ib[i] = 0;
                }
     
                /* handle single indirect block */
                if(i < *aibc)
                {
                        for(j=0; i<*aibc && j<NIDIR; j++, i++)
                                ib[j] = ib[i];
                        for(; j<NIDIR; j++)
                                ib[j] = 0;
                        ip->i_faddr[LADDR] = alloc();

                        wtfs(ip->i_faddr[LADDR], (char *)ib, s4b_idx);
                }
     
                /* handle double indirect block */
                if(i < *aibc)
                {
                        for(k=0; k<NIDIR && i<*aibc; k++)
                        {
                                for(j=0; i<*aibc && j<NIDIR; j++, i++)
                                        ib[j] = ib[i];
                                for(; j<NIDIR; j++)
                                        ib[j] = 0;
                                ib2[k] = alloc();
                                wtfs(ib2[k], (char *)ib, s4b_idx);
                        }
                        for(; k<NIDIR; k++)
                                ib2[k] = 0;
                        ip->i_faddr[LADDR+1] = alloc();
                        wtfs(ip->i_faddr[LADDR+1], (char *)ib2, s4b_idx );
                }
     
                /* triple indirect block? Nope. */
                if(i < *aibc)
                {
                        printf("triple indirect blocks not handled\n");
                }
                break;

        default:
                printf("bogus ftype %o\n", ip->i_ftype);
                exit(1);
        }

        /* convert the address list to correct disk format */
        if( doswap )
                s4ltol3r(dp->di_addr, ip->i_faddr, S4_NADDR);
        else
                s4ltol3(dp->di_addr, ip->i_faddr, S4_NADDR);
                   
        wtfs(d, buf, s4b_ino);
}