feat: upgrade LAMMPS from stable_23Jun2022 to stable_22Jul2025 (#201)

## Overview
Upgrades LAMMPS from `stable_23Jun2022_update1` to
`stable_22Jul2025_update1` (latest stable release).

## Changes

### LAMMPS Version Update (cpp/build.py)
- **LAMMPS branch**: `stable_23Jun2022_update1` →
`stable_22Jul2025_update1` (3 years of updates!)
- **Atom ID size**: Changed from `smallsmall` (32-bit IDs) to `smallbig`
(64-bit IDs) for larger system support
- **Patch application**: Fixed path to apply patch from correct
directory
- **Build fixes**: Updated emcc quoting logic to handle `]` characters

### Updated Patches (cpp/lammps.patch)
Updated patches to work with new LAMMPS API:
- **fix_ave_time.h**: Updated to use new `std::vector<value_t>` API
instead of raw arrays
- **input.h**: Updated visibility modifiers for new LAMMPS structure
- **modify.cpp**: Updated fix exception list for new LAMMPS version
- **neigh_request.h**: Maintained `friend class FixAtomify` declaration
- **Removed obsolete patches**: error.cpp, info.cpp, platform.cpp
patches no longer needed

### Code Updates (cpp/lammpsweb/atomify_fix.cpp)
- Adapted to new LAMMPS API changes in fix_ave_time
- Updated to work with `std::vector<value_t>` instead of arrays

### Binary Updates
- **public/lammps.wasm**: Recompiled with new LAMMPS version (17MB vs
10MB - newer LAMMPS has more features)
- **src/wasm/lammps.mjs**: Updated generated JavaScript bindings

## Benefits
- ✅ **3 years of LAMMPS improvements**: Bug fixes, performance
improvements, new features
- ✅ **64-bit atom IDs**: Support for larger systems (>2 billion atoms)
- ✅ **Latest stable release**: Access to most recent stable LAMMPS
features
- ✅ **Cleaner patches**: Removed obsolete patches that are no longer
needed

## Testing
- ✅ Builds successfully with Emscripten
- ✅ WebAssembly module loads correctly
- ✅ All Atomify features work with new LAMMPS version

Author: andeplane

cpp/build.py

@@ -4,6 +4,8 @@
 import hashlib
 import sys
 
+LAMMPS_BRANCH = "stable_22Jul2025_update1"
+
 # Emscripten SDK path - adjust if needed
 try:
   EMSDK_PATH = os.environ["EMSDK_PATH"]
@@ -97,7 +99,7 @@ def configure_cmake(emsdk_env, debug_mode=False):
   package_flags = [f"-DPKG_{pkg}=ON" for pkg in packages]
 
   # Common compiler flags
-  cc_flags_common = "-DLAMMPS_EXCEPTIONS -DLAMMPS_SMALLSMALL -s NO_DISABLE_EXCEPTION_CATCHING=1 -DCOLVARS_LAMMPS"
+  cc_flags_common = "-DLAMMPS_EXCEPTIONS -s NO_DISABLE_EXCEPTION_CATCHING=1 -DCOLVARS_LAMMPS"
 
   if debug_mode:
     # Debug flags
@@ -114,7 +116,7 @@ def configure_cmake(emsdk_env, debug_mode=False):
     f"-DCMAKE_BUILD_TYPE={build_type}",
     "-DCMAKE_CXX_STANDARD=17",
     "-DCMAKE_CXX_STANDARD_REQUIRED=ON",
-    "-DLAMMPS_SIZES=smallsmall",  # Use 32-bit integers (matches Makefile)
+    "-DLAMMPS_SIZES=smallbig",
     "-DBUILD_MPI=OFF",  # Use LAMMPS built-in MPI STUBS for serial build
     "-DDOWNLOAD_VORO=ON",  # Let CMake download and build Voro++ automatically
     f'-DCMAKE_CXX_FLAGS="{cc_flags}"',
@@ -198,7 +200,7 @@ def link_wasm_module(emsdk_env, debug_mode=False):
   ])
 
   # Build command with proper quoting
-  emcc_cmd = "emcc " + " ".join(f'"{arg}"' if any(c in arg for c in [" ", "=", "'", "["]) else arg for arg in emcc_args)
+  emcc_cmd = "emcc " + " ".join(f'"{arg}"' if any(c in arg for c in [" ", "'", "[", "]"]) else arg for arg in emcc_args)
   full_cmd = f'source {emsdk_env} && {emcc_cmd}'
 
   subprocess.run(full_cmd, shell=True, executable="/bin/bash", check=True)
@@ -207,7 +209,7 @@ def link_wasm_module(emsdk_env, debug_mode=False):
 if not os.path.exists('lammps'):
   # First clone lammps
   print("Could not find local clone of LAMMPS, cloning ...")
-  subprocess.run("git clone --depth 1 --branch stable_23Jun2022_update1  https://github.com/lammps/lammps.git", shell=True, check=True)
+  subprocess.run(f"git clone --depth 1 --branch {LAMMPS_BRANCH}  https://github.com/lammps/lammps.git", shell=True, check=True)
 
   # Verify lammps directory was created
   if not os.path.exists('lammps'):
@@ -224,15 +226,16 @@ def link_wasm_module(emsdk_env, debug_mode=False):
   copy_moltemplate_files()  # Custom pair styles
 
   cwd = os.getcwd()
-  print("Changing directory ...")
-  os.chdir('lammps/src')
   print("Applying patch ...")
   try:
-    subprocess.run("git apply lammps.patch", shell=True, check=True)
+    subprocess.run(["git", "apply", "src/lammps.patch"], check=True, cwd="lammps")
   except subprocess.CalledProcessError as e:
     print(f"WARNING: Patch application failed with exit code {e.returncode}")
     # Don't exit, as patch might already be applied
 
+  print("Changing directory ...")
+  os.chdir('lammps/src')
+  
   if os.path.isfile('fix_imd.cpp'):
     print("Deleting non-functioning files fix_imd ...")
     os.remove('fix_imd.cpp')

cpp/lammps.patch

@@ -1,128 +1,77 @@
-diff --git a/src/error.cpp b/src/error.cpp
-index 912093c..da78f2e 100644
---- a/src/error.cpp
-+++ b/src/error.cpp
-@@ -162,8 +162,8 @@ void Error::all(const std::string &file, int line, const std::string &str)
- 
-   if (update) update->whichflag = 0;
- 
--  std::string msg = fmt::format("ERROR: {} ({}:{})\n",
--                                str, truncpath(file), line);
-+  std::string msg = fmt::format("ERROR: {} ({}:{})\nLast command: {}",
-+                                str, truncpath(file), line, lastcmd);
- 
-   if (universe->nworlds > 1) {
-     throw LAMMPSAbortException(msg, universe->uworld);
 diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h
-index 55df82c..7df4801 100644
+index 7e16b0e..a01df02 100644
 --- a/src/fix_ave_time.h
 +++ b/src/fix_ave_time.h
-@@ -38,6 +38,12 @@ class FixAveTime : public Fix {
-   double compute_scalar() override;
+@@ -36,7 +36,6 @@ class FixAveTime : public Fix {
    double compute_vector(int) override;
    double compute_array(int, int) override;
+ 
+- private:
+   struct value_t {
+     int which;       // type of data: COMPUTE, FIX, VARIABLE
+     int argindex;    // 1-based index if data is vector, else 0
+@@ -51,6 +50,14 @@ class FixAveTime : public Fix {
+       int v;
+     } val;
+   };
++
 +  bigint nextvalid();
-+  int getmode() { return mode; }
-+  int getnvalues() { return nvalues; }
-+  int getnrows() { return nrows; }
-+  char **getids() { return ids; }
-+  int *getwhich() { return which; }
++  int getmode() const { return mode; }
++  int getnvalues() const { return nvalues; }
++  int getnrows() const { return nrows; }
++  const std::vector<value_t> &getValues() const { return values; }
++
++ private:
+   std::vector<value_t> values;
 
-  private:
-   int me, nvalues;
-@@ -77,7 +83,6 @@ class FixAveTime : public Fix {
+   int nvalues, nrepeat, nfreq, irepeat;
+@@ -84,7 +91,6 @@ class FixAveTime : public Fix {
    void invoke_vector(bigint);
    void options(int, int, char **);
    void allocate_arrays();
 -  bigint nextvalid();
  };
- 
  }    // namespace LAMMPS_NS
-diff --git a/src/info.cpp b/src/info.cpp
-index 2261b1d..71e340e 100644
---- a/src/info.cpp
-+++ b/src/info.cpp
-@@ -1326,9 +1326,9 @@ void Info::get_memory_info(double *meminfo)
- #endif
-     meminfo[1] = (double)mi.uordblks/1048576.0+(double)mi.hblkhd/1048576.0;
- #endif
--    struct rusage ru;
--    if (getrusage(RUSAGE_SELF, &ru) == 0)
--      meminfo[2] = (double)ru.ru_maxrss/1024.0;
-+    // struct rusage ru;
-+    // if (getrusage(RUSAGE_SELF, &ru) == 0)
-+    //   meminfo[2] = (double)ru.ru_maxrss/1024.0;
  #endif
- }
- 
 diff --git a/src/input.h b/src/input.h
-index f54d2ea..a78b3d6 100644
+index 949a70d..14b7ffc 100644
 --- a/src/input.h
 +++ b/src/input.h
-@@ -26,7 +26,6 @@ class Input : protected Pointers {
-   friend class Error;
-   friend class Deprecated;
-   friend class SimpleCommandsTest_Echo_Test;
--
-  public:
-   int narg;                    // # of command args
-   char **arg;                  // parsed args for command
-@@ -41,12 +40,10 @@ class Input : protected Pointers {
-   // substitute for variables in a string
-   void write_echo(const std::string &);    // send text to active echo file pointers
+@@ -44,11 +44,10 @@ class Input : protected Pointers {
+   void write_echo(const std::string &);                    // send text to active echo file pointers
+   int get_jump_skip() const { return jump_skip; }
 
 - protected:
-   char *command;      // ptr to current command
    int echo_screen;    // 0 = no, 1 = yes
    int echo_log;       // 0 = no, 1 = yes
 
-- private:
+- protected:
++
    int me;                           // proc ID
    int maxarg;                       // max # of args in arg
    char *line, *copy, *work;         // input line & copy and work string
 diff --git a/src/modify.cpp b/src/modify.cpp
-index 90b911b..8c462ba 100644
+index 5a125d7..b79f3d4 100644
 --- a/src/modify.cpp
 +++ b/src/modify.cpp
-@@ -807,7 +807,7 @@ Fix *Modify::add_fix(int narg, char **arg, int trysuffix)
-   // nullptr must be last entry in this list
- 
-   const char *exceptions[] = {"GPU",   "OMP", "INTEL",      "property/atom", "cmap",
--                              "cmap3", "rx",  "deprecated", "STORE/KIM",     nullptr};
-+                              "cmap3", "rx",  "deprecated", "STORE/KIM", "atomify",     nullptr};
+@@ -830,7 +830,7 @@ Fix *Modify::add_fix(int narg, char **arg, int trysuffix)
+   // clang-format off
+   const char *exceptions[] =
+     {"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx", "deprecated", "STORE/KIM",
+-     "amoeba/pitorsion", "amoeba/bitorsion", "DUMMY", nullptr};
++     "amoeba/pitorsion", "amoeba/bitorsion", "DUMMY", "atomify", nullptr};
+   // clang-format on
 
    if (domain->box_exist == 0) {
-     int m;
 diff --git a/src/neigh_request.h b/src/neigh_request.h
-index 71c5987..95ffa86 100644
+index caa9e05..3dc69e5 100644
 --- a/src/neigh_request.h
 +++ b/src/neigh_request.h
-@@ -27,6 +27,7 @@ class NeighRequest : protected Pointers {
-   friend class NeighborKokkos;
+@@ -28,6 +28,7 @@ class NeighRequest : protected Pointers {
    friend class NPairSkipIntel;
+   friend class NPairSkipTrimIntel;
    friend class FixIntel;
 +  friend class FixAtomify;
 
-  protected:
-   int index;                 // index of which neigh request this is
-diff --git a/src/platform.cpp b/src/platform.cpp
-index 667481b..85aee47 100644
---- a/src/platform.cpp
-+++ b/src/platform.cpp
-@@ -141,11 +141,11 @@ double platform::cputime()
- 
- #else /* ! _WIN32 */
- 
--  struct rusage ru;
--  if (getrusage(RUSAGE_SELF, &ru) == 0) {
--    rv = (double) ru.ru_utime.tv_sec;
--    rv += (double) ru.ru_utime.tv_usec * 0.000001;
--  }
-+  // struct rusage ru;
-+  // if (getrusage(RUSAGE_SELF, &ru) == 0) {
-+  //   rv = (double) ru.ru_utime.tv_sec;
-+  //   rv += (double) ru.ru_utime.tv_usec * 0.000001;
-+  // }
- 
- #endif
- 
+  public:
+   enum { REGULAR, INTRA, INTER };

cpp/lammpsweb/atomify_fix.cpp

@@ -72,10 +72,10 @@ bool Fix::trySync(LAMMPS_NS::FixAveTime *fix) {
       m_yLabel = "Value";
       return true;
     } else {
-      char **ids = fix->getids();
-      int *which = fix->getwhich();
+      const auto &values = fix->getValues();
       for(int i=0; i<nvalues; i++) {
-        auto type = getType(which[i], ids[i]);
+        const auto &val = values[i];
+        auto type = getType(val.which, val.id);
 
 
         std::string key = std::string("Value ")+std::to_string(i+1);
@@ -100,7 +100,7 @@ bool Fix::trySync(LAMMPS_NS::FixAveTime *fix) {
         m_clearPerSync = true;
 
         if(type==ComputeRDF) {
-          LAMMPS_NS::ComputeRDF *compute_rdf = dynamic_cast<LAMMPS_NS::ComputeRDF *>(m_lmp->modify->get_compute_by_id(ids[i]));
+          LAMMPS_NS::ComputeRDF *compute_rdf = dynamic_cast<LAMMPS_NS::ComputeRDF *>(m_lmp->modify->get_compute_by_id(val.id));
           for(int j=0; j<nrows; j++) {
             double binCenter = compute_rdf->array[j][0];
             double value = fix->compute_array(j, i);