From d033755561e1954b22ca82dc3e3d9922966782ec Mon Sep 17 00:00:00 2001
From: Qianqian Fang <fangqq@gmail.com>
Date: Thu, 21 Nov 2024 01:51:31 -0500
Subject: [PATCH] [bug] apply patch in #235 to pmcx, bump pmcx to v0.3.6

---
 pmcx/README.md        | 2 +-
 pmcx/pmcx/__init__.py | 2 +-
 pmcx/setup.py         | 2 +-
 src/pmcx.cpp          | 8 ++++----
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/pmcx/README.md b/pmcx/README.md
index 06c44f27..5e243b47 100644
--- a/pmcx/README.md
+++ b/pmcx/README.md
@@ -4,7 +4,7 @@
 
 - Copyright: (C) Matin Raayai Ardakani (2022-2023) <raayaiardakani.m at northeastern.edu>, Qianqian Fang (2019-2024) <q.fang at neu.edu>, Fan-Yu Yen (2023-2024) <yen.f at northeastern.edu>
 - License: GNU Public License V3 or later
-- Version: 0.3.5
+- Version: 0.3.6
 - URL: https://pypi.org/project/pmcx/
 - Github: https://github.com/fangq/mcx
 
diff --git a/pmcx/pmcx/__init__.py b/pmcx/pmcx/__init__.py
index 6761665b..2c64bb49 100644
--- a/pmcx/pmcx/__init__.py
+++ b/pmcx/pmcx/__init__.py
@@ -49,7 +49,7 @@
 # from .files import loadmc2, loadmch, load, save
 from .bench import bench
 
-__version__ = "0.3.5"
+__version__ = "0.3.6"
 
 __all__ = (
     "gpuinfo",
diff --git a/pmcx/setup.py b/pmcx/setup.py
index 71c1fe97..2fd5c22b 100644
--- a/pmcx/setup.py
+++ b/pmcx/setup.py
@@ -123,7 +123,7 @@ def build_extension(self, ext):
 setup(
     name="pmcx",
     packages=["pmcx"],
-    version="0.3.5",
+    version="0.3.6",
     requires=["numpy"],
     license="GPLv3+",
     author="Matin Raayai Ardakani, Qianqian Fang, Fan-Yu Yen",
diff --git a/src/pmcx.cpp b/src/pmcx.cpp
index 84b3ae4b..f9b78257 100644
--- a/src/pmcx.cpp
+++ b/src/pmcx.cpp
@@ -105,7 +105,7 @@ void parseVolume(const py::dict& user_cfg, Config& mcx_config) {
         free(mcx_config.vol);
     }
 
-    unsigned int dim_xyz = 0;
+    size_t dim_xyz = 0;
 
     // Data type-specific logic
     if (py::array_t<int8_t>::check_(volume_handle)) {
@@ -1091,9 +1091,9 @@ py::dict pmcx_interface(const py::dict& user_cfg) {
 
         /** Initialize all buffers necessary to store the output variables */
         if (mcx_config.issave2pt == 1) {
-            int field_len =
+            size_t field_len =
                 static_cast<int>(mcx_config.dim.x) * static_cast<int>(mcx_config.dim.y) * static_cast<int>(mcx_config.dim.z) *
-                (int) ((mcx_config.tend - mcx_config.tstart) / mcx_config.tstep + 0.5) * mcx_config.srcnum;
+                (size_t) ((mcx_config.tend - mcx_config.tstart) / mcx_config.tstep + 0.5) * mcx_config.srcnum;
 
             if (mcx_config.replay.seed != nullptr && mcx_config.replaydet == -1) {
                 field_len *= mcx_config.detnum;
@@ -1218,7 +1218,7 @@ py::dict pmcx_interface(const py::dict& user_cfg) {
         }
 
         if (mcx_config.issave2pt) {
-            int field_len;
+            size_t field_len;
             field_dim[0] = mcx_config.srcnum * mcx_config.dim.x;
             field_dim[1] = mcx_config.dim.y;
             field_dim[2] = mcx_config.dim.z;