fix bc mcxlab/pmcxcl memory error,fangq/mcx#191,fangq/mcx#192

fangq · Oct 3, 2023 · fa8dbb2 · fa8dbb2
1 parent aa5da8c
commit fa8dbb2
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Showing 4 changed files with 5 additions and 7 deletions.
diff --git a/src/mcx_utils.c b/src/mcx_utils.c
@@ -292,7 +292,7 @@ void mcx_initcfg(Config* cfg) {
     cfg->debuglevel = 0;
     cfg->gpuid = 0;
 
-    memset(cfg->bc, 0, 12);
+    memset(cfg->bc, 0, 13);
     memset(&cfg->his, 0, sizeof(History));
     memcpy(cfg->his.magic, "MCXH", 4);
     cfg->his.version = 1;

diff --git a/src/mcx_utils.h b/src/mcx_utils.h
@@ -232,7 +232,7 @@ typedef struct MCXConfig {
     int parentid;                /**<flag for testing if mcx is executed inside matlab*/
     uint optlevel;               /**<OpenCL JIT compilation optimization level*/
     uint mediabyte;              /**< how many bytes per media index, mcx supports 1, 2 and 4, 4 is the default*/
-    char bc[12];                 /**<boundary condition flag for [-x,-y,-z,+x,+y,+z, det(-x,-y,-z,+x,+y,+z)] */
+    char bc[13];                 /**<boundary condition flag for [-x,-y,-z,+x,+y,+z, det(-x,-y,-z,+x,+y,+z)], last element is always NULL for string termination */
 } Config;
 
 #ifdef  __cplusplus

diff --git a/src/mcxlabcl.cpp b/src/mcxlabcl.cpp
@@ -1034,8 +1034,7 @@ void mcx_set_field(const mxArray* root, const mxArray* item, int idx, Config* cf
             mexErrMsgTxt("the 'bc' field must be a non-empty string");
         }
 
-        mxGetString(item, cfg->bc, len + 1);
-        cfg->bc[len] = '\0';
+        mxGetString(item, cfg->bc, len + 1); // copy the string, plus the ending NULL, max 13 char
         printf("mcx.bc='%s';\n", cfg->bc);
     } else if (strcmp(name, "detphotons") == 0) {
         arraydim = mxGetDimensions(item);

diff --git a/src/pmcxcl.cpp b/src/pmcxcl.cpp
@@ -758,11 +758,10 @@ void parse_config(const py::dict& user_cfg, Config& mcx_config) {
         std::string bc_string = py::str(user_cfg["bc"]);
 
         if (bc_string.empty() || bc_string.size() > 12) {
-            throw py::value_error("the 'bc' field must be a non-empty string / have less than 12 characters.");
+            throw py::value_error("the 'bc' field must be a non-empty string / have no less than 12 characters.");
         }
 
-        strncpy(mcx_config.bc, bc_string.c_str(), bc_string.size() + 1);
-        mcx_config.bc[bc_string.size()] = '\0';
+        strncpy(mcx_config.bc, bc_string.c_str(), bc_string.size() + 1); // copy the string, plus the ending NULL, max 13 char
     }
 
     if (user_cfg.contains("detphotons")) {