//.........这里部分代码省略.........
			status_printf_ln(s, GIT_COLOR_NORMAL,
					"%s", only_include_assumed);

		ai_tmp = cut_ident_timestamp_part(author_ident->buf);
		ci_tmp = cut_ident_timestamp_part(committer_ident.buf);
		if (strcmp(author_ident->buf, committer_ident.buf))
			status_printf_ln(s, GIT_COLOR_NORMAL,
				_("%s"
				"Author:    %s"),
				ident_shown++ ? "" : "\n",
				author_ident->buf);

		if (!committer_ident_sufficiently_given())
			status_printf_ln(s, GIT_COLOR_NORMAL,
				_("%s"
				"Committer: %s"),
				ident_shown++ ? "" : "\n",
				committer_ident.buf);

		if (ident_shown)
			status_printf_ln(s, GIT_COLOR_NORMAL, "");

		saved_color_setting = s->use_color;
		s->use_color = 0;
		commitable = run_status(s->fp, index_file, prefix, 1, s);
		s->use_color = saved_color_setting;

		*ai_tmp = ' ';
		*ci_tmp = ' ';
	} else {
		unsigned char sha1[20];
		const char *parent = "HEAD";

		if (!active_nr && read_cache() < 0)
			die(_("Cannot read index"));

		if (amend)
			parent = "HEAD^1";

		if (get_sha1(parent, sha1))
			commitable = !!active_nr;
		else
			commitable = index_differs_from(parent, 0);
	}
	strbuf_release(&committer_ident);

	fclose(s->fp);

	/*
	 * Reject an attempt to record a non-merge empty commit without
	 * explicit --allow-empty. In the cherry-pick case, it may be
	 * empty due to conflict resolution, which the user should okay.
	 */
	if (!commitable && whence != FROM_MERGE && !allow_empty &&
	    !(amend && is_a_merge(current_head))) {
		s->display_comment_prefix = old_display_comment_prefix;
		run_status(stdout, index_file, prefix, 0, s);
		if (amend)
			fputs(_(empty_amend_advice), stderr);
		else if (whence == FROM_CHERRY_PICK) {
			fputs(_(empty_cherry_pick_advice), stderr);
			if (!sequencer_in_use)
				fputs(_(empty_cherry_pick_advice_single), stderr);
			else
				fputs(_(empty_cherry_pick_advice_multi), stderr);
		}

//.........这里部分代码省略.........
			(parse_opt_cb *) unresolve_callback},
		{OPTION_LOWLEVEL_CALLBACK, 'g', "again", &has_errors, NULL,
			N_("only update entries that differ from HEAD"),
			PARSE_OPT_NONEG | PARSE_OPT_NOARG,
			(parse_opt_cb *) reupdate_callback},
		OPT_BIT(0, "ignore-missing", &refresh_args.flags,
			N_("ignore files missing from worktree"),
			REFRESH_IGNORE_MISSING),
		OPT_SET_INT(0, "verbose", &verbose,
			N_("report actions to standard output"), 1),
		{OPTION_CALLBACK, 0, "clear-resolve-undo", NULL, NULL,
			N_("(for porcelains) forget saved unresolved conflicts"),
			PARSE_OPT_NOARG | PARSE_OPT_NONEG,
			resolve_undo_clear_callback},
		OPT_INTEGER(0, "index-version", &preferred_index_format,
			N_("write index in this format")),
		OPT_BOOL(0, "split-index", &split_index,
			N_("enable or disable split index")),
		OPT_END()
	};

	if (argc == 2 && !strcmp(argv[1], "-h"))
		usage_with_options(update_index_usage, options);

	git_config(git_default_config, NULL);

	/* We can't free this memory, it becomes part of a linked list parsed atexit() */
	lock_file = xcalloc(1, sizeof(struct lock_file));

	newfd = hold_locked_index(lock_file, 0);
	if (newfd < 0)
		lock_error = errno;

	entries = read_cache();
	if (entries < 0)
		die("cache corrupted");

	/*
	 * Custom copy of parse_options() because we want to handle
	 * filename arguments as they come.
	 */
	parse_options_start(&ctx, argc, argv, prefix,
			    options, PARSE_OPT_STOP_AT_NON_OPTION);
	while (ctx.argc) {
		if (parseopt_state != PARSE_OPT_DONE)
			parseopt_state = parse_options_step(&ctx, options,
							    update_index_usage);
		if (!ctx.argc)
			break;
		switch (parseopt_state) {
		case PARSE_OPT_HELP:
			exit(129);
		case PARSE_OPT_NON_OPTION:
		case PARSE_OPT_DONE:
		{
			const char *path = ctx.argv[0];
			const char *p;

			setup_work_tree();
			p = prefix_path(prefix, prefix_length, path);
			update_one(p);
			if (set_executable_bit)
				chmod_path(set_executable_bit, p);
			free((char *)p);
			ctx.argc--;
			ctx.argv++;

int cmd_rm(int argc, const char **argv, const char *prefix)
{
	int i, newfd;
	const char **pathspec;
	char *seen;

	git_config(git_default_config, NULL);

	argc = parse_options(argc, argv, prefix, builtin_rm_options,
			     builtin_rm_usage, 0);
	if (!argc)
		usage_with_options(builtin_rm_usage, builtin_rm_options);

	if (!index_only)
		setup_work_tree();

	newfd = hold_locked_index(&lock_file, 1);

	if (read_cache() < 0)
		die(_("index file corrupt"));

	/*
	 * Drop trailing directory separators from directories so we'll find
	 * submodules in the index.
	 */
	for (i = 0; i < argc; i++) {
		size_t pathlen = strlen(argv[i]);
		if (pathlen && is_dir_sep(argv[i][pathlen - 1]) &&
		    is_directory(argv[i])) {
			do {
				pathlen--;
			} while (pathlen && is_dir_sep(argv[i][pathlen - 1]));
			argv[i] = xmemdupz(argv[i], pathlen);
		}
	}

	pathspec = get_pathspec(prefix, argv);
	refresh_index(&the_index, REFRESH_QUIET, pathspec, NULL, NULL);

	seen = NULL;
	for (i = 0; pathspec[i] ; i++)
		/* nothing */;
	seen = xcalloc(i, 1);

	for (i = 0; i < active_nr; i++) {
		struct cache_entry *ce = active_cache[i];
		if (!match_pathspec(pathspec, ce->name, ce_namelen(ce), 0, seen))
			continue;
		ALLOC_GROW(list.entry, list.nr + 1, list.alloc);
		list.entry[list.nr].name = ce->name;
		list.entry[list.nr++].is_submodule = S_ISGITLINK(ce->ce_mode);
	}

	if (pathspec) {
		const char *match;
		int seen_any = 0;
		for (i = 0; (match = pathspec[i]) != NULL ; i++) {
			if (!seen[i]) {
				if (!ignore_unmatch) {
					die(_("pathspec '%s' did not match any files"),
					    match);
				}
			}
			else {
				seen_any = 1;
			}
			if (!recursive && seen[i] == MATCHED_RECURSIVELY)
				die(_("not removing '%s' recursively without -r"),
				    *match ? match : ".");
		}

		if (! seen_any)
			exit(0);
	}

	/*
	 * If not forced, the file, the index and the HEAD (if exists)
	 * must match; but the file can already been removed, since
	 * this sequence is a natural "novice" way:
	 *
	 *	rm F; git rm F
	 *
	 * Further, if HEAD commit exists, "diff-index --cached" must
	 * report no changes unless forced.
	 */
	if (!force) {
		unsigned char sha1[20];
		if (get_sha1("HEAD", sha1))
			hashclr(sha1);
		if (check_local_mod(sha1, index_only))
			exit(1);
	} else if (!index_only) {
		if (check_submodules_use_gitfiles())
			exit(1);
	}

	/*
	 * First remove the names from the index: we won't commit
	 * the index unless all of them succeed.
	 */
//.........这里部分代码省略.........

//.........这里部分代码省略.........

	} /** for **/
    } else {
       /**
	**  User wants all module ``whatis'' info
	**/

	/**
	 **  If no MODULEPATH defined, we can not output anything
	 **/
	if( !(modpath = (char *) xgetenv( "MODULEPATH")))
	    if( OK != ErrorLogger( ERR_MODULE_PATH, LOC, NULL))
		goto unwind0;

	/**
	 **  Check whether a cache file exists then list all the ``whatis'' info
	 **  Otherwise read all module files ...
	 **/
	cache_file = apropos_cache();
	if( !sw_create && cache_file && !stat( cache_file, &stats)) {

	    /**
	     **	 Open the cache file
	     **/
	    if((FILE *) NULL == (cachefp = fopen( cache_file, "r"))) {
		if( OK != ErrorLogger( ERR_OPEN, LOC, cache_file, NULL))
		    goto unwind1;
	
	    } else {
		
		/**
		 **  Read the cache and close the file
		 **/
		result = read_cache( argc, argv, cachefp, WHATIS_ALL);

		if( EOF == fclose( cachefp))
		    if( OK != ErrorLogger( ERR_CLOSE, LOC, cache_file, NULL))
			goto unwind1;

		done = 1;
	    }
	}

	/**
	 **  If we're not done now, we have to scan the files
	 **/
	 if( !done) {

	     /**
	      **  Open the cache file if neccessary
	      **/
	     if( sw_create && cache_file)
		 if((FILE *) NULL == (cachefp = fopen( cache_file, "w")))
		     if( OK != ErrorLogger( ERR_OPEN, LOC, cache_file, NULL))
			 goto unwind1;
		
	     /**
	      **  Tokenize the module path string and check all dirs
	      **/
	     for( dirname = xstrtok( modpath, ":");
		  dirname;
		  dirname = xstrtok( NULL, ":") ) {
	
		 if( !check_dir( dirname))
		     continue;
	

int mydisk_read(int start_address, int nbytes, void *buffer) {
    //TODO:
    //startBlockIdx and endBlockIdx indicate start and end block
    //of this writing operation
    //pls carefully calculate them
    int startBlockIdx = 0;
    int endBlockIdx = 0;
    int i = 0, j = 0;
    int iEndAddress = start_address + nbytes -1;
    int iCurrPosition = 0;
    int iNumberOfBlocks;
    char *cCache = (char *)malloc(BLOCK_SIZE);
    int bSeek = 0;

    startBlockIdx = start_address / BLOCK_SIZE;
    endBlockIdx = (start_address + nbytes - 1) / BLOCK_SIZE;

    iNumberOfBlocks = endBlockIdx - startBlockIdx + 1;

    // Validating that the parameters are good for the operation.
    if (start_address < 0) {
        return (1);
    } else if (nbytes < 0) {
        return (1);
    } else if ((start_address + nbytes) >= (diskEntity.max_blocks*BLOCK_SIZE) ) {
        return (1);
    }

    size_t bufferOffset = 0;

    for (i = startBlockIdx; i < endBlockIdx + 1; i++) {
        int blockInCacheFlag = 0; //0 - no, 1 - yes

        if (1 == CACHE_SWITCH) blockInCacheFlag = query_cache(i);

        // The time required to move between sector for the first block.
        if ((diskEntity.disk_type == 0) && !blockInCacheFlag && !bSeek) {
            Disk_Latency += HDD_SEEK;
            bSeek = 1;
        }
        
        if (0 == blockInCacheFlag) {
            //if cache is missed or disabled
            //TODO:read data from disk

            // Calculation for the disk latency for each block.
            if (diskEntity.disk_type == 0) {
                Disk_Latency += HDD_READ_LATENCY;
            } else if (diskEntity.disk_type == 1) {
                Disk_Latency += SSD_READ_LATENCY;
            }

            for (j = 0 ; j < BLOCK_SIZE; j++) {
                iCurrPosition = i*BLOCK_SIZE+j;
                if ((iCurrPosition >= start_address) && (iCurrPosition <= iEndAddress)) {
                    fseek(diskEntity.pBlockStore, iCurrPosition, SEEK_SET);
                    fread(buffer+bufferOffset, 1, 1, diskEntity.pBlockStore);
                    // Add the content in "cCache" to have a full block of information.
                    bufferOffset++;
                }
            }

            if (1 == CACHE_SWITCH) {
                // Add the latency for the caching.
                if (diskEntity.disk_type == 0) {
                    Disk_Latency += CACHE_WRITE_LATENCY;
                } else if (diskEntity.disk_type == 1) {
                    Disk_Latency += CACHE_WRITE_LATENCY;
                }

                // Reading the data on the disk to have the full block in the cache.
                for (j = 0 ; j < BLOCK_SIZE; j++) {
                    iCurrPosition = i*BLOCK_SIZE+j;
                    if ((iCurrPosition >= start_address) && (iCurrPosition <= iEndAddress)) {
                        // Add the content in "cCache" to have a full block of information.
                        fseek (diskEntity.pBlockStore, iCurrPosition, SEEK_SET);
                        fread(cCache+j, 1, 1, diskEntity.pBlockStore);
                    } else {
                        // Will read and store the part of the block which is not in the passed buffer
                        // to have a complete block in the cache.
                        fseek (diskEntity.pBlockStore, iCurrPosition, SEEK_SET);
                        fread(cCache+j, 1, 1, diskEntity.pBlockStore);
                    }
                }

                //TODO: if cache is enabled, cache this block
                add_cache_entry(i, cCache);
                cCache = (char *)malloc(BLOCK_SIZE);
            }
        } else {
            Disk_Latency += CACHE_READ_LATENCY;
            //if this block is cached, 
            //TODO:read this block from cache through read_cache(int)
            char *cCachedBlock = read_cache(i);
            for (j = 0 ; j < BLOCK_SIZE ; j++) {
                iCurrPosition = i*BLOCK_SIZE+j;
                if ((iCurrPosition >= start_address) && (iCurrPosition <= iEndAddress)) {
                    memset(buffer+bufferOffset, cCachedBlock[j], 1);
                    bufferOffset++;
                }
//.........这里部分代码省略.........

void
worker(int sock)
{
	int fd = -1;
	char buf[16];
	ssize_t size;
	char buf0[BUFSIZE];
	char buf1[BUFSIZE];
	char ls[LS][WS];
	int cnt0;
	int cnt1;
	const char file_name[] = "list.txt";
	int rsz;
	int k;
	std::ifstream in(file_name, std::ios::in | std::ios::binary);
	for (;;) {
		size = sock_fd_read(sock, buf, 1, &fd);
		if (fd != -1) {
			std::cout << "worker_pid = " << getpid() << std::endl;
			bzero((char *) &buf0, sizeof(buf0));
			bzero((char *) &buf1, sizeof(buf1));
			for (int i = 0; i < LS; i++)
				bzero((char *) ls[i], sizeof(ls[i]));

			rsz = recv(fd, buf0, BUFSIZE, MSG_NOSIGNAL);
			k = strlen(buf0) - 1;
			while(k >= 0 && (buf0[k] == 10 || buf0[k] == 13)) {
				buf0[k] = '\0';
				k = strlen(buf0) - 1;
			}

			sops.sem_op = -1;
			semop(semid, &sops, 1);
			cnt0 = read_cache(buf0, ls);
			sops.sem_op = 1;
			semop(semid, &sops, 1);

			if (cnt0 < LS) {
				cnt1 = read_file(in, buf0, ls, cnt0);

				sops.sem_op = -1;
				semop(semid, &sops, 1);
				write_cache(ls, cnt0, cnt1);
				sops.sem_op = 1;
				semop(semid, &sops, 1);
			} else
				cnt1 = cnt0;

			for (int i = 0; i < cnt1; i++) {
				strcat(buf1, ls[i]);
			}

			rsz = strlen(buf1);
			if (!rsz) {
				strcpy(buf1, "\n");
				rsz = 1;
			}

			send(fd, buf1, rsz, MSG_NOSIGNAL);
			close(fd);
		}
		in.seekg(0, std::ios::beg);
		sleep(5);
	}
	in.close();
}

int cmd_clean(int argc, const char **argv, const char *prefix)
{
	int i;
	int show_only = 0, remove_directories = 0, quiet = 0, ignored = 0;
	int ignored_only = 0, baselen = 0, config_set = 0, errors = 0;
	int rm_flags = REMOVE_DIR_KEEP_NESTED_GIT;
	struct strbuf directory = STRBUF_INIT;
	struct dir_struct dir;
	static const char **pathspec;
	struct strbuf buf = STRBUF_INIT;
	struct string_list exclude_list = STRING_LIST_INIT_NODUP;
	const char *qname;
	char *seen = NULL;
	struct option options[] = {
		OPT__QUIET(&quiet),
		OPT__DRY_RUN(&show_only),
		OPT_BOOLEAN('f', "force", &force, "force"),
		OPT_BOOLEAN('d', NULL, &remove_directories,
				"remove whole directories"),
		{ OPTION_CALLBACK, 'e', "exclude", &exclude_list, "pattern",
		  "exclude <pattern>", PARSE_OPT_NONEG, exclude_cb },
		OPT_BOOLEAN('x', NULL, &ignored, "remove ignored files, too"),
		OPT_BOOLEAN('X', NULL, &ignored_only,
				"remove only ignored files"),
		OPT_END()
	};

	git_config(git_clean_config, NULL);
	if (force < 0)
		force = 0;
	else
		config_set = 1;

	argc = parse_options(argc, argv, prefix, options, builtin_clean_usage,
			     0);

	memset(&dir, 0, sizeof(dir));
	if (ignored_only)
		dir.flags |= DIR_SHOW_IGNORED;

	if (ignored && ignored_only)
		die("-x and -X cannot be used together");

	if (!show_only && !force)
		die("clean.requireForce %s to true and neither -n nor -f given; "
		    "refusing to clean", config_set ? "set" : "defaults");

	if (force > 1)
		rm_flags = 0;

	dir.flags |= DIR_SHOW_OTHER_DIRECTORIES;

	if (read_cache() < 0)
		die("index file corrupt");

	if (!ignored)
		setup_standard_excludes(&dir);

	for (i = 0; i < exclude_list.nr; i++)
		add_exclude(exclude_list.items[i].string, "", 0, dir.exclude_list);

	pathspec = get_pathspec(prefix, argv);

	fill_directory(&dir, pathspec);

	if (pathspec)
		seen = xmalloc(argc > 0 ? argc : 1);

	for (i = 0; i < dir.nr; i++) {
		struct dir_entry *ent = dir.entries[i];
		int len, pos;
		int matches = 0;
		struct cache_entry *ce;
		struct stat st;

		/*
		 * Remove the '/' at the end that directory
		 * walking adds for directory entries.
		 */
		len = ent->len;
		if (len && ent->name[len-1] == '/')
			len--;
		pos = cache_name_pos(ent->name, len);
		if (0 <= pos)
			continue;	/* exact match */
		pos = -pos - 1;
		if (pos < active_nr) {
			ce = active_cache[pos];
			if (ce_namelen(ce) == len &&
			    !memcmp(ce->name, ent->name, len))
				continue; /* Yup, this one exists unmerged */
		}

		/*
		 * we might have removed this as part of earlier
		 * recursive directory removal, so lstat() here could
		 * fail with ENOENT.
		 */
		if (lstat(ent->name, &st))
			continue;
//.........这里部分代码省略.........

//.........这里部分代码省略.........
			add_excludes_from_file(&dir, argv[++i]);
			continue;
		}
		if (!prefixcmp(arg, "--exclude-from=")) {
			exc_given = 1;
			add_excludes_from_file(&dir, arg+15);
			continue;
		}
		if (!prefixcmp(arg, "--exclude-per-directory=")) {
			exc_given = 1;
			dir.exclude_per_dir = arg + 24;
			continue;
		}
		if (!strcmp(arg, "--exclude-standard")) {
			exc_given = 1;
			setup_standard_excludes(&dir);
			continue;
		}
		if (!strcmp(arg, "--full-name")) {
			prefix_offset = 0;
			continue;
		}
		if (!strcmp(arg, "--error-unmatch")) {
			error_unmatch = 1;
			continue;
		}
		if (!prefixcmp(arg, "--with-tree=")) {
			with_tree = arg + 12;
			continue;
		}
		if (!prefixcmp(arg, "--abbrev=")) {
			abbrev = strtoul(arg+9, NULL, 10);
			if (abbrev && abbrev < MINIMUM_ABBREV)
				abbrev = MINIMUM_ABBREV;
			else if (abbrev > 40)
				abbrev = 40;
			continue;
		}
		if (!strcmp(arg, "--abbrev")) {
			abbrev = DEFAULT_ABBREV;
			continue;
		}
		if (*arg == '-')
			usage(ls_files_usage);
		break;
	}

	if (require_work_tree && !is_inside_work_tree())
		setup_work_tree();

	pathspec = get_pathspec(prefix, argv + i);

	/* Verify that the pathspec matches the prefix */
	if (pathspec)
		prefix = verify_pathspec(prefix);

	/* Treat unmatching pathspec elements as errors */
	if (pathspec && error_unmatch) {
		int num;
		for (num = 0; pathspec[num]; num++)
			;
		ps_matched = xcalloc(1, num);
	}

	if (dir.show_ignored && !exc_given) {
		fprintf(stderr, "%s: --ignored needs some exclude pattern\n",
			argv[0]);
		exit(1);
	}

	/* With no flags, we default to showing the cached files */
	if (!(show_stage | show_deleted | show_others | show_unmerged |
	      show_killed | show_modified))
		show_cached = 1;

	read_cache();
	if (prefix)
		prune_cache(prefix);
	if (with_tree) {
		/*
		 * Basic sanity check; show-stages and show-unmerged
		 * would not make any sense with this option.
		 */
		if (show_stage || show_unmerged)
			die("ls-files --with-tree is incompatible with -s or -u");
		overlay_tree_on_cache(with_tree, prefix);
	}
	show_files(&dir, prefix);

	if (ps_matched) {
		int bad;
		bad = report_path_error(ps_matched, pathspec, prefix_offset);
		if (bad)
			fprintf(stderr, "Did you forget to 'git add'?\n");

		return bad ? 1 : 0;
	}

	return 0;
}

//.........这里部分代码省略.........
		OPT_INTEGER(0, "index-version", &preferred_index_format,
			N_("write index in this format")),
		OPT_BOOL(0, "split-index", &split_index,
			N_("enable or disable split index")),
		OPT_BOOL(0, "untracked-cache", &untracked_cache,
			N_("enable/disable untracked cache")),
		OPT_SET_INT(0, "test-untracked-cache", &untracked_cache,
			    N_("test if the filesystem supports untracked cache"), UC_TEST),
		OPT_SET_INT(0, "force-untracked-cache", &untracked_cache,
			    N_("enable untracked cache without testing the filesystem"), UC_FORCE),
		OPT_SET_INT(0, "force-write-index", &force_write,
			N_("write out the index even if is not flagged as changed"), 1),
		OPT_BOOL(0, "fsmonitor", &fsmonitor,
			N_("enable or disable file system monitor")),
		{OPTION_SET_INT, 0, "fsmonitor-valid", &mark_fsmonitor_only, NULL,
			N_("mark files as fsmonitor valid"),
			PARSE_OPT_NOARG | PARSE_OPT_NONEG, NULL, MARK_FLAG},
		{OPTION_SET_INT, 0, "no-fsmonitor-valid", &mark_fsmonitor_only, NULL,
			N_("clear fsmonitor valid bit"),
			PARSE_OPT_NOARG | PARSE_OPT_NONEG, NULL, UNMARK_FLAG},
		OPT_END()
	};

	if (argc == 2 && !strcmp(argv[1], "-h"))
		usage_with_options(update_index_usage, options);

	git_config(git_default_config, NULL);

	/* we will diagnose later if it turns out that we need to update it */
	newfd = hold_locked_index(&lock_file, 0);
	if (newfd < 0)
		lock_error = errno;

	entries = read_cache();
	if (entries < 0)
		die("cache corrupted");

	/*
	 * Custom copy of parse_options() because we want to handle
	 * filename arguments as they come.
	 */
	parse_options_start(&ctx, argc, argv, prefix,
			    options, PARSE_OPT_STOP_AT_NON_OPTION);
	while (ctx.argc) {
		if (parseopt_state != PARSE_OPT_DONE)
			parseopt_state = parse_options_step(&ctx, options,
							    update_index_usage);
		if (!ctx.argc)
			break;
		switch (parseopt_state) {
		case PARSE_OPT_HELP:
		case PARSE_OPT_ERROR:
			exit(129);
		case PARSE_OPT_NON_OPTION:
		case PARSE_OPT_DONE:
		{
			const char *path = ctx.argv[0];
			char *p;

			setup_work_tree();
			p = prefix_path(prefix, prefix_length, path);
			update_one(p);
			if (set_executable_bit)
				chmod_path(set_executable_bit, p);
			free(p);
			ctx.argc--;

int cmd_checkout_index(int argc, const char **argv, const char *prefix)
{
	int i;
	struct lock_file lock_file = LOCK_INIT;
	int all = 0;
	int read_from_stdin = 0;
	int prefix_length;
	int force = 0, quiet = 0, not_new = 0;
	int index_opt = 0;
	struct option builtin_checkout_index_options[] = {
		OPT_BOOL('a', "all", &all,
			N_("check out all files in the index")),
		OPT__FORCE(&force, N_("force overwrite of existing files"), 0),
		OPT__QUIET(&quiet,
			N_("no warning for existing files and files not in index")),
		OPT_BOOL('n', "no-create", &not_new,
			N_("don't checkout new files")),
		OPT_BOOL('u', "index", &index_opt,
			 N_("update stat information in the index file")),
		OPT_BOOL('z', NULL, &nul_term_line,
			N_("paths are separated with NUL character")),
		OPT_BOOL(0, "stdin", &read_from_stdin,
			N_("read list of paths from the standard input")),
		OPT_BOOL(0, "temp", &to_tempfile,
			N_("write the content to temporary files")),
		OPT_STRING(0, "prefix", &state.base_dir, N_("string"),
			N_("when creating files, prepend <string>")),
		{ OPTION_CALLBACK, 0, "stage", NULL, "(1|2|3|all)",
			N_("copy out the files from named stage"),
			PARSE_OPT_NONEG, option_parse_stage },
		OPT_END()
	};

	if (argc == 2 && !strcmp(argv[1], "-h"))
		usage_with_options(builtin_checkout_index_usage,
				   builtin_checkout_index_options);
	git_config(git_default_config, NULL);
	prefix_length = prefix ? strlen(prefix) : 0;

	if (read_cache() < 0) {
		die("invalid cache");
	}

	argc = parse_options(argc, argv, prefix, builtin_checkout_index_options,
			builtin_checkout_index_usage, 0);
	state.istate = &the_index;
	state.force = force;
	state.quiet = quiet;
	state.not_new = not_new;

	if (!state.base_dir)
		state.base_dir = "";
	state.base_dir_len = strlen(state.base_dir);

	/*
	 * when --prefix is specified we do not want to update cache.
	 */
	if (index_opt && !state.base_dir_len && !to_tempfile) {
		state.refresh_cache = 1;
		state.istate = &the_index;
		hold_locked_index(&lock_file, LOCK_DIE_ON_ERROR);
	}

	/* Check out named files first */
	for (i = 0; i < argc; i++) {
		const char *arg = argv[i];
		char *p;

		if (all)
			die("git checkout-index: don't mix '--all' and explicit filenames");
		if (read_from_stdin)
			die("git checkout-index: don't mix '--stdin' and explicit filenames");
		p = prefix_path(prefix, prefix_length, arg);
		checkout_file(p, prefix);
		free(p);
	}

	if (read_from_stdin) {
		struct strbuf buf = STRBUF_INIT;
		struct strbuf unquoted = STRBUF_INIT;
		strbuf_getline_fn getline_fn;

		if (all)
			die("git checkout-index: don't mix '--all' and '--stdin'");

		getline_fn = nul_term_line ? strbuf_getline_nul : strbuf_getline_lf;
		while (getline_fn(&buf, stdin) != EOF) {
			char *p;
			if (!nul_term_line && buf.buf[0] == '"') {
				strbuf_reset(&unquoted);
				if (unquote_c_style(&unquoted, buf.buf, NULL))
					die("line is badly quoted");
				strbuf_swap(&buf, &unquoted);
			}
			p = prefix_path(prefix, prefix_length, buf.buf);
			checkout_file(p, prefix);
			free(p);
		}
		strbuf_release(&unquoted);
		strbuf_release(&buf);
//.........这里部分代码省略.........

/*
 * Merge the commits h1 and h2, return the resulting virtual
 * commit object and a flag indicating the cleanness of the merge.
 */
int merge_recursive(struct merge_options *o,
		    struct commit *h1,
		    struct commit *h2,
		    struct commit_list *ca,
		    struct commit **result)
{
	struct commit_list *iter;
	struct commit *merged_common_ancestors;
	struct tree *mrtree = mrtree;
	int clean;

	if (show(o, 4)) {
		output(o, 4, "Merging:");
		output_commit_title(o, h1);
		output_commit_title(o, h2);
	}

	if (!ca) {
		ca = get_merge_bases(h1, h2, 1);
		ca = reverse_commit_list(ca);
	}

	if (show(o, 5)) {
		output(o, 5, "found %u common ancestor(s):", commit_list_count(ca));
		for (iter = ca; iter; iter = iter->next)
			output_commit_title(o, iter->item);
	}

	merged_common_ancestors = pop_commit(&ca);
	if (merged_common_ancestors == NULL) {
		/* if there is no common ancestor, make an empty tree */
		struct tree *tree = xcalloc(1, sizeof(struct tree));

		tree->object.parsed = 1;
		tree->object.type = OBJ_TREE;
		pretend_sha1_file(NULL, 0, OBJ_TREE, tree->object.sha1);
		merged_common_ancestors = make_virtual_commit(tree, "ancestor");
	}

	for (iter = ca; iter; iter = iter->next) {
		const char *saved_b1, *saved_b2;
		o->call_depth++;
		/*
		 * When the merge fails, the result contains files
		 * with conflict markers. The cleanness flag is
		 * ignored, it was never actually used, as result of
		 * merge_trees has always overwritten it: the committed
		 * "conflicts" were already resolved.
		 */
		discard_cache();
		saved_b1 = o->branch1;
		saved_b2 = o->branch2;
		o->branch1 = "Temporary merge branch 1";
		o->branch2 = "Temporary merge branch 2";
		merge_recursive(o, merged_common_ancestors, iter->item,
				NULL, &merged_common_ancestors);
		o->branch1 = saved_b1;
		o->branch2 = saved_b2;
		o->call_depth--;

		if (!merged_common_ancestors)
			die("merge returned no commit");
	}

	discard_cache();
	if (!o->call_depth)
		read_cache();

	clean = merge_trees(o, h1->tree, h2->tree, merged_common_ancestors->tree,
			    &mrtree);

	if (o->call_depth) {
		*result = make_virtual_commit(mrtree, "merged tree");
		commit_list_insert(h1, &(*result)->parents);
		commit_list_insert(h2, &(*result)->parents->next);
	}
	flush_output(o);
	return clean;
}

int cmd_rm(int argc, const char **argv, const char *prefix)
{
	int i;
	struct pathspec pathspec;
	char *seen;

	gitmodules_config();
	git_config(git_default_config, NULL);

	argc = parse_options(argc, argv, prefix, builtin_rm_options,
			     builtin_rm_usage, 0);
	if (!argc)
		usage_with_options(builtin_rm_usage, builtin_rm_options);

	if (!index_only)
		setup_work_tree();

	hold_locked_index(&lock_file, 1);

	if (read_cache() < 0)
		die(_("index file corrupt"));

	parse_pathspec(&pathspec, 0,
		       PATHSPEC_PREFER_CWD |
		       PATHSPEC_STRIP_SUBMODULE_SLASH_CHEAP,
		       prefix, argv);
	refresh_index(&the_index, REFRESH_QUIET, &pathspec, NULL, NULL);

	seen = xcalloc(pathspec.nr, 1);

	for (i = 0; i < active_nr; i++) {
		const struct cache_entry *ce = active_cache[i];
		if (!ce_path_match(ce, &pathspec, seen))
			continue;
		ALLOC_GROW(list.entry, list.nr + 1, list.alloc);
		list.entry[list.nr].name = xstrdup(ce->name);
		list.entry[list.nr].is_submodule = S_ISGITLINK(ce->ce_mode);
		if (list.entry[list.nr++].is_submodule &&
		    !is_staging_gitmodules_ok())
			die (_("Please stage your changes to .gitmodules or stash them to proceed"));
	}

	if (pathspec.nr) {
		const char *original;
		int seen_any = 0;
		for (i = 0; i < pathspec.nr; i++) {
			original = pathspec.items[i].original;
			if (!seen[i]) {
				if (!ignore_unmatch) {
					die(_("pathspec '%s' did not match any files"),
					    original);
				}
			}
			else {
				seen_any = 1;
			}
			if (!recursive && seen[i] == MATCHED_RECURSIVELY)
				die(_("not removing '%s' recursively without -r"),
				    *original ? original : ".");
		}

		if (!seen_any)
			exit(0);
	}

	/*
	 * If not forced, the file, the index and the HEAD (if exists)
	 * must match; but the file can already been removed, since
	 * this sequence is a natural "novice" way:
	 *
	 *	rm F; git rm F
	 *
	 * Further, if HEAD commit exists, "diff-index --cached" must
	 * report no changes unless forced.
	 */
	if (!force) {
		unsigned char sha1[20];
		if (get_sha1("HEAD", sha1))
			hashclr(sha1);
		if (check_local_mod(sha1, index_only))
			exit(1);
	} else if (!index_only) {
		if (check_submodules_use_gitfiles())
			exit(1);
	}

	/*
	 * First remove the names from the index: we won't commit
	 * the index unless all of them succeed.
	 */
	for (i = 0; i < list.nr; i++) {
		const char *path = list.entry[i].name;
		if (!quiet)
			printf("rm '%s'\n", path);

		if (remove_file_from_cache(path))
			die(_("git rm: unable to remove %s"), path);
	}

	if (show_only)
//.........这里部分代码省略.........

//.........这里部分代码省略.........
                      {
                        std::cerr << " iter, training file changed " << std::endl;
                        training_file = "bbe";
                      }
          */
          /*
                if ( ii == 1000 )
                  {
                    std::cerr << " iter, training file changed " << std::endl;
                    samu.set_training_file ( "bbe" );
                  }
                else if ( ii == 1000 + 4000 )
                  {
                    std::cerr << " iter, training file changed " << std::endl;
                    training_file = "none";
                    samu.set_training_file ( training_file );
                  }
                else if ( ii == 1000 + 4000 + 5000 )
                  {
                    std::cerr << " iter, training file changed " << std::endl;
                    samu.set_training_file ( "bbe" );
                  }
                else if ( ii == 1000 + 4000 + 5000 + 4000 )
                  {
                    std::cerr << " iter, training file changed " << std::endl;
                    training_file = "none";
                    samu.set_training_file ( training_file );
                  }
                  */
#endif

          samu.clear_vi();
          if ( samu.get_training_file() == training_file )
            {
              samu.set_N_e ( N_e );
              for ( int i {0}; i<test_triplets["introduce myself"].size() && samu.sleep(); ++i )
                {
                  SPOTriplets tv;
                  tv.push_back ( test_triplets["introduce myself"][i] );
                  sum += to_samu ( 11, tv );
                  ++cnt;
                  brel += samu.get_brel();
                }
            }
          else
            {
              samu.set_N_e ( N_e );
              std::string key = samu.get_training_file();

              if ( cache.find ( key ) == cache.end() )
                {

                  std::fstream triplet_train ( key+".triplets",  std::ios_base::in );
                  if ( triplet_train )
                    {

                      do
                        {

                          SPOTriplet t;
                          triplet_train >> t;

                          if ( !t.empty() )
                            cache[key].push_back ( t );

                        }
                      while ( !triplet_train.eof() && samu.sleep() );

                      triplet_train.close();

                      sum = read_cache ( key, cnt, brel );

                    }
                  else
                    {

                      std::fstream train ( samu.get_training_file(),  std::ios_base::in );
                      if ( train )
                        {
                          std::string file = key+".triplets";
                          for ( std::string line; std::getline ( train, line ) && samu.sleep(); )
                            {

#ifndef TRIPLET_CACHE
                              sum += to_samu ( 12, line );
#else
                              sum += to_samu ( 12, line, file );
#endif
                              ++cnt;
                              brel += samu.get_brel();

                            }
                          train.close();
                        }

                    }

                }
              else
                {

                              sum += to_samu ( 12, line, file );
#endif
                              ++cnt;
                              brel += samu.get_brel();

                            }
                          train.close();
                        }

                    }

                }
              else
                {

                  sum = read_cache ( key, cnt, brel );

                }

            }

          //std::cerr << "###### " << ++j << "-th iter " << sum << std::endl;

          double mbrel = ( double ) brel/ ( double ) cnt;
          int bad = ( sum - samu.get_max_reward() * cnt ) / ( samu.get_min_reward() - samu.get_max_reward() );
          std::cerr << ++j
                    << "-th iter, err: "
                    << cnt*samu.get_max_reward() - sum
                    << " ("
                    << sum
                    << ", good: "

static int do_apply_stash(const char *prefix, struct stash_info *info,
			  int index, int quiet)
{
	int ret;
	int has_index = index;
	struct merge_options o;
	struct object_id c_tree;
	struct object_id index_tree;
	struct commit *result;
	const struct object_id *bases[1];

	read_cache_preload(NULL);
	if (refresh_cache(REFRESH_QUIET))
		return -1;

	if (write_cache_as_tree(&c_tree, 0, NULL))
		return error(_("cannot apply a stash in the middle of a merge"));

	if (index) {
		if (oideq(&info->b_tree, &info->i_tree) ||
		    oideq(&c_tree, &info->i_tree)) {
			has_index = 0;
		} else {
			struct strbuf out = STRBUF_INIT;

			if (diff_tree_binary(&out, &info->w_commit)) {
				strbuf_release(&out);
				return error(_("could not generate diff %s^!."),
					     oid_to_hex(&info->w_commit));
			}

			ret = apply_cached(&out);
			strbuf_release(&out);
			if (ret)
				return error(_("conflicts in index."
					       "Try without --index."));

			discard_cache();
			read_cache();
			if (write_cache_as_tree(&index_tree, 0, NULL))
				return error(_("could not save index tree"));

			reset_head();
		}
	}

	if (info->has_u && restore_untracked(&info->u_tree))
		return error(_("could not restore untracked files from stash"));

	init_merge_options(&o, the_repository);

	o.branch1 = "Updated upstream";
	o.branch2 = "Stashed changes";

	if (oideq(&info->b_tree, &c_tree))
		o.branch1 = "Version stash was based on";

	if (quiet)
		o.verbosity = 0;

	if (o.verbosity >= 3)
		printf_ln(_("Merging %s with %s"), o.branch1, o.branch2);

	bases[0] = &info->b_tree;

	ret = merge_recursive_generic(&o, &c_tree, &info->w_tree, 1, bases,
				      &result);
	if (ret) {
		rerere(0);

		if (index)
			fprintf_ln(stderr, _("Index was not unstashed."));

		return ret;
	}

	if (has_index) {
		if (reset_tree(&index_tree, 0, 0))
			return -1;
	} else {
		struct strbuf out = STRBUF_INIT;

		if (get_newly_staged(&out, &c_tree)) {
			strbuf_release(&out);
			return -1;
		}

		if (reset_tree(&c_tree, 0, 1)) {
			strbuf_release(&out);
			return -1;
		}

		ret = update_index(&out);
		strbuf_release(&out);
		if (ret)
			return -1;

		discard_cache();
	}

//.........这里部分代码省略.........

int cmd_check_attr(int argc, const char **argv, const char *prefix)
{
    struct git_attr_check *check;
    int cnt, i, doubledash, filei;

    argc = parse_options(argc, argv, prefix, check_attr_options,
                         check_attr_usage, PARSE_OPT_KEEP_DASHDASH);

    if (read_cache() < 0) {
        die("invalid cache");
    }

    if (cached_attrs)
        git_attr_set_direction(GIT_ATTR_INDEX, NULL);

    doubledash = -1;
    for (i = 0; doubledash < 0 && i < argc; i++) {
        if (!strcmp(argv[i], "--"))
            doubledash = i;
    }

    /* Process --all and/or attribute arguments: */
    if (all_attrs) {
        if (doubledash >= 1)
            error_with_usage("Attributes and --all both specified");

        cnt = 0;
        filei = doubledash + 1;
    } else if (doubledash == 0) {
        error_with_usage("No attribute specified");
    } else if (doubledash < 0) {
        if (!argc)
            error_with_usage("No attribute specified");

        if (stdin_paths) {
            /* Treat all arguments as attribute names. */
            cnt = argc;
            filei = argc;
        } else {
            /* Treat exactly one argument as an attribute name. */
            cnt = 1;
            filei = 1;
        }
    } else {
        cnt = doubledash;
        filei = doubledash + 1;
    }

    /* Check file argument(s): */
    if (stdin_paths) {
        if (filei < argc)
            error_with_usage("Can't specify files with --stdin");
    } else {
        if (filei >= argc)
            error_with_usage("No file specified");
    }

    if (all_attrs) {
        check = NULL;
    } else {
        check = xcalloc(cnt, sizeof(*check));
        for (i = 0; i < cnt; i++) {
            const char *name;
            struct git_attr *a;
            name = argv[i];
            a = git_attr(name);
            if (!a)
                return error("%s: not a valid attribute name",
                             name);
            check[i].attr = a;
        }
    }

    if (stdin_paths)
        check_attr_stdin_paths(prefix, cnt, check);
    else {
        for (i = filei; i < argc; i++)
            check_attr(prefix, cnt, check, argv[i]);
        maybe_flush_or_die(stdout, "attribute to stdout");
    }
    return 0;
}

}

template <int dimension, typename float_type>
void verlet_nvt_andersen<dimension, float_type>::set_temperature(double temperature)
{
    temperature_ = temperature;
    sqrt_temperature_ = std::sqrt(temperature_);
    LOG("temperature of heat bath: " << temperature_);
}

template <int dimension, typename float_type>
void verlet_nvt_andersen<dimension, float_type>::integrate()
{
    LOG_TRACE("update