From e24142649331244c0b83a43c7feb6e0063643692 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Wed, 18 Feb 2026 03:33:52 +0100 Subject: [PATCH 01/22] feat(readcon): replace con2matter FILE* parser with readcon-core Use readcon-core (https://github.com/lode-org/readcon-core) v0.2.0 as a meson subproject for reading .con files. The hand-written sscanf/fgets parser is replaced by readcon::ConFrameIterator which delegates to the Rust-based parser. - Add subprojects/readcon-core.wrap pinned to v0.2.0 - Link readcon-core statically into eonclib - Replace Matter::con2matter(FILE*) with Matter::con2matter(ConFrame&) - Bump meson_version to >= 1.8.0 (required by readcon-core's Rust support) - Add rust >= 1.88 to pixi base dependencies - Add ensure_cbindgen pixi task (cbindgen not yet on conda-forge) - matter2con and convel2matter remain FILE*-based (readcon-core lacks a frame-builder API) Entire-Checkpoint: c0e7b0158776 --- client/Matter.cpp | 178 +- client/Matter.h | 5 +- client/meson.build | 12 + docs/source/devdocs/design/client/confile.md | 37 + docs/source/devdocs/design/client/index.md | 1 + meson.build | 2 +- pixi.lock | 5752 +++++------------- pixi.toml | 3 + subprojects/readcon-core.wrap | 8 + 9 files changed, 1620 insertions(+), 4378 deletions(-) create mode 100644 docs/source/devdocs/design/client/confile.md create mode 100644 subprojects/readcon-core.wrap diff --git a/client/Matter.cpp b/client/Matter.cpp index 9a93850ec..e5acff32e 100644 --- a/client/Matter.cpp +++ b/client/Matter.cpp @@ -644,54 +644,45 @@ bool Matter::matter2con(FILE *file) { return true; } -// Load atomic coordinates from a .con file +// Load atomic coordinates from a .con file via readcon-core bool Matter::con2matter(std::string filename) { - bool state; - FILE *file; // Add the .con extension to filename if it is not already there. int pos = filename.find_last_of('.'); if (filename.compare(pos + 1, 3, "con")) { filename += ".con"; } - file = fopen(filename.c_str(), "rb"); - if (!file) { - SPDLOG_LOGGER_ERROR(m_log, "File {} was not found.", filename); - return (false); + try { + readcon::ConFrameIterator frames(filename); + auto it = frames.begin(); + if (!(it != frames.end())) { + SPDLOG_LOGGER_ERROR(m_log, "No frames found in {}", filename); + return false; + } + return con2matter(*it); + } catch (const std::exception &e) { + SPDLOG_LOGGER_ERROR(m_log, "Failed to read {}: {}", filename, e.what()); + return false; } - state = con2matter(file); - fclose(file); - return (state); } -bool Matter::con2matter(FILE *file) { - char line[255]; // Temporary string of character to read from the file. - fgets(headerCon1, sizeof(line), file); - - // if (strchr(headerCon1,'\r')) { - // /* Files created on Windows or on Mac with Excell have carriage - // returns (\r) instead of or along with the new line charater (\n). C - // recognises only the \n as the end of line. */ cerr << "A carriage - // return ('\\r') has been detected. To work correctly, new lines - // should be indicated by the new line character (\\n)."; return false; - // // return false for error - // } - - long int i; - int j; - - fgets(headerCon2, sizeof(line), file); - - double lengths[3]; - // The third line contains the length of the periodic cell - fgets(line, sizeof(line), file); - sscanf(line, "%lf %lf %lf", &lengths[0], &lengths[1], &lengths[2]); - - double angles[3]; - fgets(headerCon4, sizeof(line), file); - // The fourth line contains the angles of the cell vectors - sscanf(headerCon4, "%lf %lf %lf", &angles[0], &angles[1], &angles[2]); - +// Populate Matter from a parsed readcon frame +bool Matter::con2matter(const readcon::ConFrame &frame) { + const auto &atoms = frame.atoms(); + const auto &lengths = frame.cell(); + const auto &angles_deg = frame.angles(); + const auto &prebox = frame.prebox_header(); + const auto &postbox = frame.postbox_header(); + + // Store headers for round-tripping via matter2con + snprintf(headerCon1, sizeof(headerCon1), "%s\n", prebox[0].c_str()); + snprintf(headerCon2, sizeof(headerCon2), "%s\n", prebox[1].c_str()); + snprintf(headerCon5, sizeof(headerCon5), "%s\n", postbox[0].c_str()); + snprintf(headerCon6, sizeof(headerCon6), "%s\n", postbox[1].c_str()); + + // Build cell matrix from lengths and angles + double angles[3] = {angles_deg[0], angles_deg[1], angles_deg[2]}; if (angles[0] == 90.0 && angles[1] == 90.0 && angles[2] == 90.0) { + cell.setZero(); cell(0, 0) = lengths[0]; cell(1, 1) = lengths[1]; cell(2, 2) = lengths[2]; @@ -716,112 +707,25 @@ bool Matter::con2matter(FILE *file) { } cellInverse = cell.inverse(); - fgets(headerCon5, sizeof(line), file); - fgets(headerCon6, sizeof(line), file); - - fgets(line, sizeof(line), file); - int Ncomponent; // Number of components or different types of atoms (eg - // water: two components H and O) - if (sscanf(line, "%d", &Ncomponent) == 0) { - SPDLOG_LOGGER_INFO(m_log, "The number of components cannot be read. One " - "component is assumed instead"); - Ncomponent = 1; - } - if ((Ncomponent > MAXC) || (Ncomponent < 1)) { - SPDLOG_LOGGER_ERROR( - m_log, - "con2atoms doesn't support more that {} components or less than 1", - MAXC); - return false; - } - - // stores the position of the first atom of each element - // 'MAXC+1': the last element is used to store the total number of atom - long int first[MAXC + 1]; - long int Natoms = 0; - first[0] = 0; - - // Now we want to know the number of atom of each type. Ex with H2O, two - // hydrogens and one oxygen - fgets(line, sizeof(line), file); - // split at either space or tab - char *split = strtok(line, " \t"); - for (j = 0; j < Ncomponent; j++) { - if (split == NULL) { - SPDLOG_LOGGER_ERROR( - m_log, "input con file does not list the number of each component"); - return false; - } - if (sscanf(split, "%ld", &Natoms) != 1) { - SPDLOG_LOGGER_ERROR( - m_log, "input con file does not list the number of each component"); - return false; - } - first[j + 1] = Natoms + first[j]; - // split at either space or tab - split = strtok(NULL, " \t"); - } - - // Set the total number of atoms, and allocates memory - resize(first[Ncomponent]); + // Also store headerCon4 for convel round-tripping + snprintf(headerCon4, sizeof(headerCon4), "%f %f %f\n", angles_deg[0], + angles_deg[1], angles_deg[2]); - double mass[MAXC]; - fgets(line, sizeof(line), file); - // split at either space or tab - split = strtok(line, " \t"); - - for (j = 0; j < Ncomponent; j++) { - // Now we want to know the number of atom of each type. Ex with - // H2O, two hydrogens and one oxygen - if (split == NULL) { - SPDLOG_LOGGER_ERROR(m_log, "input con file does not list enough masses"); - return false; - } - // *1* seems like a bug as a result of copying and pasting from above - // *1* if(sscanf(split, "%ld", &Natoms)!=1) - if (sscanf(split, "%lf", &mass[j]) != 1) { - SPDLOG_LOGGER_ERROR(m_log, "input con file does not list enough masses"); - return false; - } - // *1* sscanf(line, "%lf", &mass[j]); - // split at either space or tab - split = strtok(NULL, " \t"); + resize(static_cast(atoms.size())); + for (size_t i = 0; i < atoms.size(); ++i) { + positions(i, 0) = atoms[i].x; + positions(i, 1) = atoms[i].y; + positions(i, 2) = atoms[i].z; + setMass(i, atoms[i].mass); + setAtomicNr(i, static_cast(atoms[i].atomic_number)); + setFixed(i, atoms[i].is_fixed ? 1 : 0); } - int atomicNr; - int fixed; - double x, y, z; - for (j = 0; j < Ncomponent; j++) { - char symbol[3]; - fgets(line, sizeof(line), file); - sscanf(line, "%2s", symbol); - atomicNr = symbol2atomicNumber(symbol); - fgets(line, sizeof(line), file); // skip one line - for (i = first[j]; i < first[j + 1]; i++) { - setMass(i, mass[j]); - - setAtomicNr(i, atomicNr); - fgets(line, sizeof(line), file); - if (strlen(line) < 6) { - SPDLOG_LOGGER_ERROR(m_log, "error parsing position in con file"); - return false; - } - - sscanf(line, "%lf %lf %lf %d\n", &x, &y, &z, &fixed); - positions(i, 0) = x; - positions(i, 1) = y; - positions(i, 2) = z; - setFixed(i, static_cast(fixed)); - } - } if (usePeriodicBoundaries) { - // Transform the coordinate to use the minimum - // image convention. applyPeriodicBoundary(); } - // potential_ = new Potential(parameters_); recomputePotential = true; - return (true); + return true; } void Matter::computePotential() { diff --git a/client/Matter.h b/client/Matter.h index c9bcc2ae2..af203a9ff 100644 --- a/client/Matter.h +++ b/client/Matter.h @@ -15,6 +15,7 @@ #include "Potential.h" #include "SurrogatePotential.h" #include +#include #include // This is a forward declaration of BondBoost to avoid a circular dependency. @@ -163,8 +164,8 @@ class Matter { void writeTibble(std::string filename); bool con2matter(std::string filename); // read con file into Matter, return // true if successful - bool con2matter(FILE *file); // read con file and load data into Matter, - // return true if successful + bool con2matter(const readcon::ConFrame &frame); // populate from a parsed + // readcon frame bool convel2matter(std::string filename); // read con file with both coordinates // and velocities into Matter diff --git a/client/meson.build b/client/meson.build index c9d236c7b..3a4f07615 100644 --- a/client/meson.build +++ b/client/meson.build @@ -582,6 +582,18 @@ endif _linkto += potentials +# readcon-core: Rust-based .con file I/O (required) +readcon_proj = subproject( + 'readcon-core', + default_options: { + 'with_tests': false, + 'with_examples': false, + 'default_library': 'static', + }, +) +readcon_dep = readcon_proj.get_variable('readcon_dep') +_deps += [readcon_dep] + # --------------------- Library eclib = library( diff --git a/docs/source/devdocs/design/client/confile.md b/docs/source/devdocs/design/client/confile.md new file mode 100644 index 000000000..b76735fd1 --- /dev/null +++ b/docs/source/devdocs/design/client/confile.md @@ -0,0 +1,37 @@ +--- +myst: + html_meta: + "description": "How eOn reads and writes .con files using the readcon-core Rust library." + "keywords": "eOn, readcon-core, .con file, Rust FFI, con2matter, matter2con" +--- + +# .con file I/O + +eOn uses [readcon-core](https://github.com/lode-org/readcon-core), a Rust +library with C/C++ FFI, for reading `.con` files. The library is included as a +Meson subproject via `subprojects/readcon-core.wrap`. + +## Reading (`con2matter`) + +`Matter::con2matter(std::string)` opens the file through +`readcon::ConFrameIterator` and extracts the first frame. +`Matter::con2matter(const readcon::ConFrame &)` then populates positions, cell, +masses, atomic numbers and fixed-atom flags from the frame's cached data. + +## Writing (`matter2con`) + +Writing is still handled by `Matter::matter2con` using `FILE *` I/O, because +readcon-core's writer can only serialise opaque `RKRConFrame` handles that +originated from a previous read. Once readcon-core gains a frame-builder API, +the write path can be migrated as well. + +## Build requirements + +readcon-core requires **Rust >= 1.88** and **cbindgen >= 0.29**. The Rust +toolchain is provided by `conda-forge` (`rust` package); cbindgen is installed +via `cargo install cbindgen` if not already present (see the `ensure_cbindgen` +pixi task). + +```{versionadded} 2.11 +Replaced the hand-written C `sscanf`/`fgets` parser with readcon-core. +``` diff --git a/docs/source/devdocs/design/client/index.md b/docs/source/devdocs/design/client/index.md index e34ca7b18..a42f80ca7 100644 --- a/docs/source/devdocs/design/client/index.md +++ b/docs/source/devdocs/design/client/index.md @@ -14,4 +14,5 @@ Guidelines and rationale for the `C++` core of eOn. :caption: Components types +confile ``` diff --git a/meson.build b/meson.build index 7499acc0b..737f63758 100644 --- a/meson.build +++ b/meson.build @@ -4,7 +4,7 @@ project( 'eon', 'cpp', version: run_command(['tools/gitversion.py'], check: true).stdout().strip(), - meson_version: '>= 1.6.0', + meson_version: '>= 1.8.0', default_options: [ # 'buildtype=debugoptimized', 'warning_level=0', diff --git a/pixi.lock b/pixi.lock index e430fea54..207c713cf 100644 --- a/pixi.lock +++ b/pixi.lock @@ -97,6 +97,8 @@ environments: - 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typer>=0.23.1 requires_python: '>=3.9' -- pypi: https://files.pythonhosted.org/packages/a7/24/5480c20380dfd18cf33d14784096dca45a24eae6102e91d49a718d3b6855/typer_slim-0.24.0-py3-none-any.whl - name: typer-slim - version: 0.24.0 - sha256: d5d7ee1ee2834d5020c7c616ed5e0d0f29b9a4b1dd283bdebae198ec09778d0e - requires_dist: - - typer>=0.24.0 - requires_python: '>=3.10' - pypi: https://download.pytorch.org/whl/typing_extensions-4.15.0-py3-none-any.whl name: typing-extensions version: 4.15.0 diff --git a/pixi.toml b/pixi.toml index cdce88fd7..3099e5739 100644 --- a/pixi.toml +++ b/pixi.toml @@ -8,6 +8,8 @@ platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"] version = "2.11.0" [tasks] +# cbindgen is not on conda-forge; install via cargo if missing +ensure_cbindgen = "command -v cbindgen >/dev/null 2>&1 || cargo install cbindgen" [dependencies] eigen = ">=3.4,<3.5" @@ -29,6 +31,7 @@ spdlog = ">=1.16,<2" pkg-config = ">=0.29.2,<0.30" fortran-compiler = ">=1.10.0,<2" pyyaml = "*" +rust = ">=1.88" sccache = "*" [pypi-dependencies] diff --git a/subprojects/readcon-core.wrap b/subprojects/readcon-core.wrap new file mode 100644 index 000000000..bd41e2af2 --- /dev/null +++ b/subprojects/readcon-core.wrap @@ -0,0 +1,8 @@ +[wrap-git] +directory = readcon-core +url = https://github.com/lode-org/readcon-core.git +revision = v0.2.0 +depth = 1 + +[provide] +readcon-core = readcon_dep From 374f57f2c524814a81d742823d0d92da03689540 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 11:56:21 +0100 Subject: [PATCH 02/22] feat(con): replace all FILE* con I/O with readcon-core v0.4.1 Replace matter2con(FILE*), matter2convel(FILE*), and convel2matter(FILE*) with readcon ConFrameBuilder, ConFrameWriter, and mmap reader. Adds cell_to_lengths_angles() helper. Uses precision=17 for .con roundtrip and precision=6 for .convel. Also speeds up con2matter by using read_first_frame (mmap) instead of the iterator path. --- client/Matter.cpp | 428 ++++++++-------------------------- client/Matter.h | 19 +- subprojects/readcon-core.wrap | 2 +- 3 files changed, 104 insertions(+), 345 deletions(-) diff --git a/client/Matter.cpp b/client/Matter.cpp index e5acff32e..86460d871 100644 --- a/client/Matter.cpp +++ b/client/Matter.cpp @@ -543,122 +543,79 @@ void Matter::matter2xyz(std::string filename, fclose(file); } +std::pair, std::array> +Matter::cell_to_lengths_angles() const { + std::array lengths; + lengths[0] = cell.row(0).norm(); + lengths[1] = cell.row(1).norm(); + lengths[2] = cell.row(2).norm(); + std::array angles; + angles[0] = acos(cell.row(0).dot(cell.row(1)) / lengths[0] / lengths[1]) * + 180.0 / helper_functions::pi; + angles[1] = acos(cell.row(0).dot(cell.row(2)) / lengths[0] / lengths[2]) * + 180.0 / helper_functions::pi; + angles[2] = acos(cell.row(1).dot(cell.row(2)) / lengths[1] / lengths[2]) * + 180.0 / helper_functions::pi; + return {lengths, angles}; +} + // Print atomic coordinates to a .con file bool Matter::matter2con(std::string filename, bool append) { - bool state; - FILE *file; int pos = filename.find_last_of('.'); if (filename.compare(pos + 1, 3, "con")) { filename += ".con"; - }; - if (append) { - file = fopen(filename.c_str(), "ab"); - } else { - file = fopen(filename.c_str(), "wb"); } - state = matter2con(file); - fclose(file); - return (state); -} - -bool Matter::matter2con(FILE *file) { - long int i; - int j; - long int Nfix = 0; // Nfix to store the number of fixed atoms - int Ncomponent = 0; // used to store the number of components (eg water: two - // components H and O) - int first[MAXC]; // to store the position of the first atom of each component - // plus at the end the total number of atoms - double mass[MAXC]; - long atomicNrs[MAXC]; - first[0] = 0; if (usePeriodicBoundaries) { - applyPeriodicBoundary(); // Transform the coordinate to use the minimum - // image convention. + applyPeriodicBoundary(); } - if (numberOfAtoms() > 0) { - if (getFixed(0)) - Nfix = 1; // count the number of fixed atoms - mass[0] = getMass(0); - atomicNrs[0] = getAtomicNr(0); + auto [lengths, angles_deg] = cell_to_lengths_angles(); + + // Strip trailing newlines from header buffers for readcon + auto strip_nl = [](const char *s) -> std::string { + std::string str(s); + while (!str.empty() && (str.back() == '\n' || str.back() == '\r')) + str.pop_back(); + return str; }; - j = 0; - for (i = 1; i < numberOfAtoms(); i++) { - if (getFixed(i)) - Nfix++; // count the number of fixed atoms - if (getAtomicNr(i) != - atomicNrs[j]) { // check if there is a second component - j++; - if (j >= MAXC) { - SPDLOG_LOGGER_ERROR(m_log, - "Does not support more than {} components and the " - "atoms must be ordered by component.", - MAXC); - return false; - }; - mass[j] = getMass(i); - atomicNrs[j] = getAtomicNr(i); - first[j] = i; - } - } - first[j + 1] = numberOfAtoms(); - Ncomponent = j + 1; - fputs(headerCon1, file); - fputs(headerCon2, file); - double lengths[3]; - lengths[0] = cell.row(0).norm(); - lengths[1] = cell.row(1).norm(); - lengths[2] = cell.row(2).norm(); - fprintf(file, "%f\t%f\t%f\n", lengths[0], lengths[1], lengths[2]); - double angles[3]; - angles[0] = acos(cell.row(0).dot(cell.row(1)) / lengths[0] / lengths[1]) * - 180 / helper_functions::pi; - angles[1] = acos(cell.row(0).dot(cell.row(2)) / lengths[0] / lengths[2]) * - 180 / helper_functions::pi; - angles[2] = acos(cell.row(1).dot(cell.row(2)) / lengths[1] / lengths[2]) * - 180 / helper_functions::pi; - fprintf(file, "%f\t%f\t%f\n", angles[0], angles[1], angles[2]); - fputs(headerCon5, file); - fputs(headerCon6, file); - - fprintf(file, "%d\n", Ncomponent); - for (j = 0; j < Ncomponent; j++) { - fprintf(file, "%d ", first[j + 1] - first[j]); - } - fprintf(file, "\n"); - for (j = 0; j < Ncomponent; j++) { - fprintf(file, "%f ", mass[j]); + readcon::ConFrameBuilder builder( + {lengths[0], lengths[1], lengths[2]}, + {angles_deg[0], angles_deg[1], angles_deg[2]}, + {strip_nl(headerCon1), strip_nl(headerCon2)}, + {strip_nl(headerCon5), strip_nl(headerCon6)}); + + for (long i = 0; i < numberOfAtoms(); i++) { + builder.add_atom(atomicNumber2symbol(getAtomicNr(i)), getPosition(i, 0), + getPosition(i, 1), getPosition(i, 2), getFixed(i) != 0, + static_cast(i), getMass(i)); } - fprintf(file, "\n"); - for (j = 0; j < Ncomponent; j++) { - fprintf(file, "%s\n", atomicNumber2symbol(atomicNrs[j])); - fprintf(file, "Coordinates of Component %d\n", j + 1); - for (i = first[j]; i < first[j + 1]; i++) { - fprintf(file, "%22.17f %22.17f %22.17f %d %4ld\n", getPosition(i, 0), - getPosition(i, 1), getPosition(i, 2), getFixed(i), i); + + auto frame = builder.build(); + std::vector frames; + if (append) { + try { + frames = readcon::read_all_frames(filename); + } catch (...) { + // File doesn't exist yet, start fresh } } + frames.push_back(std::move(frame)); + readcon::ConFrameWriter writer(filename, 17); + writer.extend(frames); return true; } -// Load atomic coordinates from a .con file via readcon-core +// Load atomic coordinates from a .con file via readcon-core (mmap reader) bool Matter::con2matter(std::string filename) { - // Add the .con extension to filename if it is not already there. int pos = filename.find_last_of('.'); if (filename.compare(pos + 1, 3, "con")) { filename += ".con"; } try { - readcon::ConFrameIterator frames(filename); - auto it = frames.begin(); - if (!(it != frames.end())) { - SPDLOG_LOGGER_ERROR(m_log, "No frames found in {}", filename); - return false; - } - return con2matter(*it); + auto frame = readcon::read_first_frame(filename); + return con2matter(frame); } catch (const std::exception &e) { SPDLOG_LOGGER_ERROR(m_log, "Failed to read {}: {}", filename, e.what()); return false; @@ -848,267 +805,70 @@ AtomMatrix Matter::getAccelerations() { Matrix Matter::getMasses() const { return masses; } bool Matter::matter2convel(std::string filename) { - bool state; - FILE *file; int pos = filename.find_last_of('.'); if (filename.compare(pos + 1, 6, "convel")) { filename += ".convel"; } - file = fopen(filename.c_str(), "w"); - state = matter2convel(file); - fclose(file); - return (state); -} - -bool Matter::matter2convel(FILE *file) { - long int i; - int j; - long int Nfix = 0; // Nfix to store the number of fixed atoms - int Ncomponent = 0; // used to store the number of components (eg water: two - // components H and O) - int first[MAXC]; // to store the position of the first atom of each component - // plus at the end the total number of atoms - double mass[MAXC]; - long atomicNrs[MAXC]; - first[0] = 0; if (usePeriodicBoundaries) { - applyPeriodicBoundary(); // Transform the coordinate to use the minimum - // image convention. + applyPeriodicBoundary(); } - if (numberOfAtoms() > 0) { - if (getFixed(0)) - Nfix = 1; // count the number of fixed atoms - mass[0] = getMass(0); - atomicNrs[0] = getAtomicNr(0); - } - j = 0; - for (i = 1; i < numberOfAtoms(); i++) { - if (getFixed(i)) - Nfix++; // count the number of fixed atoms - if (getAtomicNr(i) != - atomicNrs[j]) { // check if there is a second component - j++; - if (j >= MAXC) { - SPDLOG_LOGGER_ERROR(m_log, - "Does not support more than {} components and the " - "atoms must be ordered by component.", - MAXC); - return false; - } - mass[j] = getMass(i); - atomicNrs[j] = getAtomicNr(i); - first[j] = i; - } - } - first[j + 1] = numberOfAtoms(); - Ncomponent = j + 1; + auto [lengths, angles_deg] = cell_to_lengths_angles(); - fputs(headerCon1, file); - fputs(headerCon2, file); - double lengths[3]; - lengths[0] = cell.row(0).norm(); - lengths[1] = cell.row(1).norm(); - lengths[2] = cell.row(2).norm(); - fprintf(file, "%f\t%f\t%f\n", lengths[0], lengths[1], lengths[2]); - double angles[3]; - angles[0] = acos(cell.row(0).dot(cell.row(1)) / lengths[0] / lengths[1]) * - 180 / helper_functions::pi; - angles[1] = acos(cell.row(0).dot(cell.row(2)) / lengths[0] / lengths[2]) * - 180 / helper_functions::pi; - angles[2] = acos(cell.row(1).dot(cell.row(2)) / lengths[1] / lengths[2]) * - 180 / helper_functions::pi; - fprintf(file, "%f\t%f\t%f\n", angles[0], angles[1], angles[2]); - fputs(headerCon5, file); - fputs(headerCon6, file); - - fprintf(file, "%d\n", Ncomponent); - for (j = 0; j < Ncomponent; j++) { - fprintf(file, "%d ", first[j + 1] - first[j]); - } - fprintf(file, "\n"); - for (j = 0; j < Ncomponent; j++) { - // mass[j]/=G_PER_MOL; // GH: I don't understand why we need to convert the - // mass units - fprintf(file, "%f ", mass[j]); - } - fprintf(file, "\n"); - for (j = 0; j < Ncomponent; j++) { - fprintf(file, "%s\n", atomicNumber2symbol(atomicNrs[j])); - fprintf(file, "Coordinates of Component %d\n", j + 1); - for (i = first[j]; i < first[j + 1]; i++) { - fprintf(file, "%11.6f\t%11.6f\t%11.6f\t%d\t%ld\n", getPosition(i, 0), - getPosition(i, 1), getPosition(i, 2), getFixed(i), i); - } - } - fprintf(file, "\n"); - for (j = 0; j < Ncomponent; j++) { - fprintf(file, "%s\n", atomicNumber2symbol(atomicNrs[j])); - fprintf(file, "Velocities of Component %d\n", j + 1); - for (i = first[j]; i < first[j + 1]; i++) { - fprintf(file, "%11.6f\t%11.6f\t%11.6f\t%d\t%ld\n", velocities(i, 0), - velocities(i, 1), velocities(i, 2), getFixed(i), i); - } - } + auto strip_nl = [](const char *s) -> std::string { + std::string str(s); + while (!str.empty() && (str.back() == '\n' || str.back() == '\r')) + str.pop_back(); + return str; + }; + + readcon::ConFrameBuilder builder( + {lengths[0], lengths[1], lengths[2]}, + {angles_deg[0], angles_deg[1], angles_deg[2]}, + {strip_nl(headerCon1), strip_nl(headerCon2)}, + {strip_nl(headerCon5), strip_nl(headerCon6)}); + + for (long i = 0; i < numberOfAtoms(); i++) { + builder.add_atom_with_velocity( + atomicNumber2symbol(getAtomicNr(i)), getPosition(i, 0), + getPosition(i, 1), getPosition(i, 2), getFixed(i) != 0, + static_cast(i), getMass(i), velocities(i, 0), + velocities(i, 1), velocities(i, 2)); + } + + auto frame = builder.build(); + readcon::ConFrameWriter writer(filename, 6); + std::vector frames; + frames.push_back(std::move(frame)); + writer.extend(frames); return true; } bool Matter::convel2matter(std::string filename) { - bool state; - FILE *file; - // Add the .con extension to filename if it is not already there. int pos = filename.find_last_of('.'); if (filename.compare(pos + 1, 3, "con")) { filename += ".con"; } - file = fopen(filename.c_str(), "rb"); - if (!file) { - SPDLOG_LOGGER_ERROR(m_log, "File {} was not found.", filename); - return (false); - } - state = convel2matter(file); - fclose(file); - return (state); -} - -bool Matter::convel2matter(FILE *file) { - char line[255]; // Temporary string of character to read from the file. - fgets(headerCon1, sizeof(line), file); - - // if (strchr(headerCon1,'\r')) { - // /* Files created on Windows or on Mac with Excell have carriage - // returns (\r) instead of or along with the new line charater (\n). C - // recognises only the \n as the end of line. */ cerr << "A carriage - // return ('\\r') has been detected. To work correctly, new lines - // should be indicated by the new line character (\\n)."; return false; - // // return false for error - // } - - long int i; - int j; - - fgets(headerCon2, sizeof(line), file); - - double lengths[3]; - // The third line contains the length of the periodic cell - fgets(line, sizeof(line), file); - sscanf(line, "%lf %lf %lf", &lengths[0], &lengths[1], &lengths[2]); - - double angles[3]; - fgets(headerCon4, sizeof(line), file); - // The fourth line contains the angles of the cell vectors - sscanf(headerCon4, "%lf %lf %lf", &angles[0], &angles[1], &angles[2]); - - if (angles[0] == 90.0 && angles[1] == 90.0 && angles[2] == 90.0) { - cell(0, 0) = lengths[0]; - cell(1, 1) = lengths[1]; - cell(2, 2) = lengths[2]; - } else { - angles[0] *= helper_functions::pi / 180.0; - angles[1] *= helper_functions::pi / 180.0; - angles[2] *= helper_functions::pi / 180.0; - - cell(0, 0) = 1.0; - cell(1, 0) = cos(angles[0]); - cell(1, 1) = sin(angles[0]); - cell(2, 0) = cos(angles[1]); - cell(2, 1) = (cos(angles[2]) - cell(1, 0) * cell(2, 0)) / cell(1, 1); - cell(2, 2) = sqrt(1.0 - pow(cell(2, 0), 2) - pow(cell(2, 1), 2)); - - cell(0, 0) *= lengths[0]; - cell(1, 0) *= lengths[1]; - cell(1, 1) *= lengths[1]; - cell(2, 0) *= lengths[2]; - cell(2, 1) *= lengths[2]; - cell(2, 2) *= lengths[2]; - } - cellInverse = cell.inverse(); - - fgets(headerCon5, sizeof(line), file); - fgets(headerCon6, sizeof(line), file); - - fgets(line, sizeof(line), file); - int Ncomponent; // Number of components or different types of atoms. For - // instance H2O has two components (H and O). - if (sscanf(line, "%d", &Ncomponent) == 0) { - SPDLOG_LOGGER_INFO(m_log, "The number of components cannot be read. One " - "component is assumed instead"); - Ncomponent = 1; - } - if ((Ncomponent > MAXC) || (Ncomponent < 1)) { - SPDLOG_LOGGER_ERROR( - m_log, - "con2atoms doesn't support more that {} components or less than 1", - MAXC); - return false; - } - /* to store the position of the - first atom of each element 'MAXC+1': the last element is used to store the - total number of atom.*/ - long int first[MAXC + 1]; - long int Natoms = 0; - first[0] = 0; - - // Now we want to know the number of atom of each type. Ex with H2O, two - // hydrogens and one oxygen - for (j = 0; j < Ncomponent; j++) { - fscanf(file, "%ld", &Natoms); - first[j + 1] = Natoms + first[j]; - } - - fgets(line, sizeof(line), file); // Discard the rest of the line - // Set the total number of atoms, and allocates memory - resize(first[Ncomponent]); - double mass[MAXC]; - for (j = 0; j < Ncomponent; j++) { - // Now we want to know the number of atom of each type. Ex with - // H2O, two hydrogens and one oxygen - fscanf(file, "%lf", &mass[j]); - // mass[j]*=G_PER_MOL; // conversion of g/mol to local units. (see su.h) - } - - fgets(line, sizeof(line), file); // discard rest of the line - int atomicNr; - int fixed; - double x, y, z; - for (j = 0; j < Ncomponent; j++) { - char symbol[3]; - fgets(line, sizeof(line), file); - sscanf(line, "%2s\n", symbol); - atomicNr = symbol2atomicNumber(symbol); - fgets(line, sizeof(line), file); // skip one line - for (i = first[j]; i < first[j + 1]; i++) { - setMass(i, mass[j]); - setAtomicNr(i, atomicNr); - fgets(line, sizeof(line), file); - sscanf(line, "%lf %lf %lf %d\n", &x, &y, &z, &fixed); - setPosition(i, 0, x); - setPosition(i, 1, y); - setPosition(i, 2, z); - setFixed(i, static_cast(fixed)); - } - } - - fgets(line, sizeof(line), file); - for (j = 0; j < Ncomponent; j++) { - fgets(line, sizeof(line), file); - fgets(line, sizeof(line), file); // skip one line - for (i = first[j]; i < first[j + 1]; i++) { - fgets(line, sizeof(line), file); - sscanf(line, "%lf %lf %lf %d\n", &x, &y, &z, &fixed); - setVelocity(i, 0, x); - setVelocity(i, 1, y); - setVelocity(i, 2, z); + try { + auto frame = readcon::read_first_frame(filename); + bool ok = con2matter(frame); + if (!ok) + return false; + if (frame.has_velocities()) { + const auto &atoms = frame.atoms(); + for (size_t i = 0; i < atoms.size(); ++i) { + setVelocity(i, 0, atoms[i].vx); + setVelocity(i, 1, atoms[i].vy); + setVelocity(i, 2, atoms[i].vz); + } } + return true; + } catch (const std::exception &e) { + SPDLOG_LOGGER_ERROR(m_log, "Failed to read convel {}: {}", filename, + e.what()); + return false; } - - if (usePeriodicBoundaries) { - applyPeriodicBoundary(); // Transform the coordinate to use the minimum - // image convention. - } - // potential_ = new Potential(parameters_); - return (true); } void Matter::writeTibble(std::string fname) { diff --git a/client/Matter.h b/client/Matter.h index af203a9ff..b347aedce 100644 --- a/client/Matter.h +++ b/client/Matter.h @@ -14,8 +14,10 @@ #include "Parameters.h" #include "Potential.h" #include "SurrogatePotential.h" +#include #include #include +#include #include // This is a forward declaration of BondBoost to avoid a circular dependency. @@ -167,19 +169,12 @@ class Matter { bool con2matter(const readcon::ConFrame &frame); // populate from a parsed // readcon frame bool - convel2matter(std::string filename); // read con file with both coordinates - // and velocities into Matter - bool convel2matter(FILE *file); // read con file with both coordinates and - // velocities and load data into Matter + convel2matter(std::string filename); // read convel file via readcon-core bool matter2con(std::string filename, - bool append = false); // print con file from data in Class Matter - bool matter2con(FILE *file); // print con file from data in Class Matter + bool append = false); // write con file via readcon-core bool - matter2convel(std::string filename); // print con file with both coordinates - // and velocities in Class Matter - bool matter2convel(FILE *file); // print con file with both coordinates and - // velocities from data in Class Matter + matter2convel(std::string filename); // write convel file via readcon-core void matter2xyz(std::string filename, bool append = false); // print xyz file from data in Matter AtomMatrix getFree() const; @@ -208,6 +203,10 @@ class Matter { void applyPeriodicBoundary(double &component, int axis); void applyPeriodicBoundary(AtomMatrix &diff); + // Extract cell lengths and angles (degrees) from the cell matrix + std::pair, std::array> + cell_to_lengths_angles() const; + // Stuff which used to be in MatterPrivateData const Parameters *parameters; long nAtoms; diff --git a/subprojects/readcon-core.wrap b/subprojects/readcon-core.wrap index bd41e2af2..2cf3b5499 100644 --- a/subprojects/readcon-core.wrap +++ b/subprojects/readcon-core.wrap @@ -1,7 +1,7 @@ [wrap-git] directory = readcon-core url = https://github.com/lode-org/readcon-core.git -revision = v0.2.0 +revision = v0.4.1 depth = 1 [provide] From a0dd59604b006cc0d8911487985711f573045871 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 11:56:31 +0100 Subject: [PATCH 03/22] refactor(con): remove FILE* usage from all con I/O call sites Convert all callers of matter2con(FILE*) to use the string filename overload directly. For multi-frame NEB paths, use the append parameter instead of manually opening a file handle. --- client/BasinHoppingJob.cpp | 6 ++---- client/DynamicsJob.cpp | 6 +----- client/GPSurrogateJob.cpp | 4 +--- client/NudgedElasticBand.cpp | 4 +--- client/NudgedElasticBandJob.cpp | 6 ++---- client/ProcessSearchJob.cpp | 14 ++++---------- client/SaddleSearchJob.cpp | 6 ++---- client/SafeHyperJob.cpp | 18 ++++-------------- client/TADJob.cpp | 18 ++++-------------- 9 files changed, 21 insertions(+), 61 deletions(-) diff --git a/client/BasinHoppingJob.cpp b/client/BasinHoppingJob.cpp index 75693257e..98f399a52 100644 --- a/client/BasinHoppingJob.cpp +++ b/client/BasinHoppingJob.cpp @@ -265,7 +265,7 @@ std::vector BasinHoppingJob::run(void) { /* Save Results */ - FILE *fileResults, *fileProduct; + FILE *fileResults; std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); @@ -295,9 +295,7 @@ std::vector BasinHoppingJob::run(void) { std::string productFilename("min.con"); returnFiles.push_back(productFilename); - fileProduct = fopen(productFilename.c_str(), "wb"); - minimumEnergyStructure->matter2con(fileProduct); - fclose(fileProduct); + minimumEnergyStructure->matter2con(productFilename); std::string bhFilename("bh.dat"); returnFiles.push_back(bhFilename); diff --git a/client/DynamicsJob.cpp b/client/DynamicsJob.cpp index 8362ce452..7170aec93 100644 --- a/client/DynamicsJob.cpp +++ b/client/DynamicsJob.cpp @@ -30,13 +30,9 @@ std::vector DynamicsJob::run(void) { d->run(); *F = *R; - FILE *fileProduct; std::string productFilename("final.con"); returnFiles.push_back(productFilename); - - fileProduct = fopen(productFilename.c_str(), "wb"); - F->matter2con(fileProduct); - fclose(fileProduct); + F->matter2con(productFilename); delete d; diff --git a/client/GPSurrogateJob.cpp b/client/GPSurrogateJob.cpp index 2e4372588..c455ea6c5 100644 --- a/client/GPSurrogateJob.cpp +++ b/client/GPSurrogateJob.cpp @@ -89,11 +89,9 @@ std::vector GPSurrogateJob::run(void) { std::string nebFilename(fmt::format("neb_final_gpr_{:03d}.con", n_gp)); returnFiles.push_back(nebFilename); - FILE *fileNEB = fopen(nebFilename.c_str(), "wb"); for (long i = 0; i <= neb->numImages + 1; i++) { - neb->path[i]->matter2con(fileNEB); + neb->path[i]->matter2con(nebFilename, /*append=*/i > 0); } - fclose(fileNEB); // } else if (status_neb == NudgedElasticBand::NEBStatus::GOOD && helper_functions::surrogate::accuratePES(neb->path, pot)) { diff --git a/client/NudgedElasticBand.cpp b/client/NudgedElasticBand.cpp index 23995cde5..519dcc8e2 100644 --- a/client/NudgedElasticBand.cpp +++ b/client/NudgedElasticBand.cpp @@ -307,11 +307,9 @@ NudgedElasticBand::NEBStatus NudgedElasticBand::compute(void) { bool append = (iteration != 0); path[maxEnergyImage]->matter2con("neb_maximage.con", append); std::string nebFilename(fmt::format("neb_path_{:03d}.con", iteration)); - FILE *fileNEBPath = fopen(nebFilename.c_str(), "wb"); for (long idx = 0; idx <= numImages + 1; idx++) { - path[idx]->matter2con(fileNEBPath); + path[idx]->matter2con(nebFilename, /*append=*/idx > 0); } - fclose(fileNEBPath); printImageData(true, iteration); } diff --git a/client/NudgedElasticBandJob.cpp b/client/NudgedElasticBandJob.cpp index 79b7b4a19..1ba2668d7 100644 --- a/client/NudgedElasticBandJob.cpp +++ b/client/NudgedElasticBandJob.cpp @@ -135,7 +135,7 @@ std::vector NudgedElasticBandJob::run(void) { void NudgedElasticBandJob::saveData(NudgedElasticBand::NEBStatus status, NudgedElasticBand *neb) { - FILE *fileResults, *fileNEB; + FILE *fileResults; std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); @@ -182,11 +182,9 @@ void NudgedElasticBandJob::saveData(NudgedElasticBand::NEBStatus status, // Save the Full NEB Path std::string nebFilename("neb.con"); returnFiles.push_back(nebFilename); - fileNEB = fopen(nebFilename.c_str(), "wb"); for (long i = 0; i <= neb->numImages + 1; i++) { - neb->path[i]->matter2con(fileNEB); + neb->path[i]->matter2con(nebFilename, /*append=*/i > 0); } - fclose(fileNEB); // Save Discrete Saddle Point (Highest Energy Image) std::string spFilename("sp.con"); diff --git a/client/ProcessSearchJob.cpp b/client/ProcessSearchJob.cpp index e510ff7e2..3489f8c66 100644 --- a/client/ProcessSearchJob.cpp +++ b/client/ProcessSearchJob.cpp @@ -235,7 +235,7 @@ int ProcessSearchJob::doProcessSearch(void) { } void ProcessSearchJob::saveData(int status) { - FILE *fileResults, *fileReactant, *fileSaddle, *fileProduct, *fileMode; + FILE *fileResults, *fileMode; std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); @@ -288,27 +288,21 @@ void ProcessSearchJob::saveData(int status) { std::string reactantFilename("reactant.con"); returnFiles.push_back(reactantFilename); - fileReactant = fopen(reactantFilename.c_str(), "wb"); - min1->matter2con(fileReactant); + min1->matter2con(reactantFilename); std::string modeFilename("mode.dat"); returnFiles.push_back(modeFilename); fileMode = fopen(modeFilename.c_str(), "wb"); helper_functions::saveMode(fileMode, saddle, saddleSearch->getEigenvector()); fclose(fileMode); - fclose(fileReactant); std::string saddleFilename("saddle.con"); returnFiles.push_back(saddleFilename); - fileSaddle = fopen(saddleFilename.c_str(), "wb"); - saddle->matter2con(fileSaddle); - fclose(fileSaddle); + saddle->matter2con(saddleFilename); std::string productFilename("product.con"); returnFiles.push_back(productFilename); - fileProduct = fopen(productFilename.c_str(), "wb"); - min2->matter2con(fileProduct); - fclose(fileProduct); + min2->matter2con(productFilename); return; } diff --git a/client/SaddleSearchJob.cpp b/client/SaddleSearchJob.cpp index 5cc9f914d..3896a7d41 100644 --- a/client/SaddleSearchJob.cpp +++ b/client/SaddleSearchJob.cpp @@ -96,7 +96,7 @@ int SaddleSearchJob::doSaddleSearch() { } void SaddleSearchJob::saveData(int status) { - FILE *fileResults, *fileSaddle, *fileMode; + FILE *fileResults, *fileMode; std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); @@ -142,9 +142,7 @@ void SaddleSearchJob::saveData(int status) { std::string saddleFilename("saddle.con"); returnFiles.push_back(saddleFilename); - fileSaddle = fopen(saddleFilename.c_str(), "wb"); - saddle->matter2con(fileSaddle); - fclose(fileSaddle); + saddle->matter2con(saddleFilename); } void SaddleSearchJob::printEndState(int status) { diff --git a/client/SafeHyperJob.cpp b/client/SafeHyperJob.cpp index 71a853510..f250a5055 100644 --- a/client/SafeHyperJob.cpp +++ b/client/SafeHyperJob.cpp @@ -286,7 +286,7 @@ int SafeHyperJob::dynamics() { } void SafeHyperJob::saveData(int status) { - FILE *fileResults, *fileReactant; + FILE *fileResults; std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); @@ -330,27 +330,17 @@ void SafeHyperJob::saveData(int status) { std::string reactantFilename("reactant.con"); returnFiles.push_back(reactantFilename); - fileReactant = fopen(reactantFilename.c_str(), "wb"); - reactant->matter2con(fileReactant); - fclose(fileReactant); + reactant->matter2con(reactantFilename); if (newStateFlag) { - FILE *fileProduct; std::string productFilename("product.con"); returnFiles.push_back(productFilename); - - fileProduct = fopen(productFilename.c_str(), "wb"); - product->matter2con(fileProduct); - fclose(fileProduct); + product->matter2con(productFilename); if (params.parallel_replica_options.refine_transition) { - FILE *fileSaddle; std::string saddleFilename("saddle.con"); returnFiles.push_back(saddleFilename); - - fileSaddle = fopen(saddleFilename.c_str(), "wb"); - saddle->matter2con(fileSaddle); - fclose(fileSaddle); + saddle->matter2con(saddleFilename); } } return; diff --git a/client/TADJob.cpp b/client/TADJob.cpp index 7dda999aa..9930b551a 100644 --- a/client/TADJob.cpp +++ b/client/TADJob.cpp @@ -276,7 +276,7 @@ int TADJob::dynamics() { } void TADJob::saveData(int status) { - FILE *fileResults, *fileReactant; + FILE *fileResults; std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); @@ -320,27 +320,17 @@ void TADJob::saveData(int status) { std::string reactantFilename("reactant.con"); returnFiles.push_back(reactantFilename); - fileReactant = fopen(reactantFilename.c_str(), "wb"); - reactant->matter2con(fileReactant); - fclose(fileReactant); + reactant->matter2con(reactantFilename); if (newStateFlag) { - FILE *fileProduct; std::string productFilename("product.con"); returnFiles.push_back(productFilename); - - fileProduct = fopen(productFilename.c_str(), "wb"); - product->matter2con(fileProduct); - fclose(fileProduct); + product->matter2con(productFilename); if (params.parallel_replica_options.refine_transition) { - FILE *fileSaddle; std::string saddleFilename("saddle.con"); returnFiles.push_back(saddleFilename); - - fileSaddle = fopen(saddleFilename.c_str(), "wb"); - saddle->matter2con(fileSaddle); - fclose(fileSaddle); + saddle->matter2con(saddleFilename); } } return; From b68d7073fa6c63366ea21d8c27aa0f47003d28b8 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 12:17:58 +0100 Subject: [PATCH 04/22] refactor: replace FILE*/fprintf with fmt::output_file across all Job files Replace all FILE*/fprintf/fclose patterns with fmt::output_file and .print() in every Job file. Also modernize saveMode in HelperFunctions to take a filename string, replace fopen-for-existence-check with std::filesystem::exists, and convert GlobalOptimizationJob member FILE* to fmt::ostream. --- client/BasinHoppingJob.cpp | 80 +++++++++++++---------------- client/DynamicsJob.cpp | 1 - client/FiniteDifferenceJob.cpp | 17 +++---- client/GlobalOptimizationJob.cpp | 8 +-- client/GlobalOptimizationJob.h | 17 +++---- client/HelperFunctions.cpp | 9 ++-- client/HelperFunctions.h | 3 +- client/HessianJob.cpp | 13 ++--- client/MinModeSaddleSearch.cpp | 4 +- client/MinimizationJob.cpp | 4 +- client/MonteCarloJob.cpp | 20 ++------ client/NudgedElasticBandJob.cpp | 83 +++++++++++++----------------- client/ParallelReplicaJob.cpp | 56 ++++++++++----------- client/PrefactorJob.cpp | 21 ++++---- client/ProcessSearchJob.cpp | 86 +++++++++++++------------------- client/ReplicaExchangeJob.cpp | 27 ++++------ client/SaddleSearchJob.cpp | 64 ++++++++---------------- client/SafeHyperJob.cpp | 61 ++++++++++------------ client/TADJob.cpp | 61 ++++++++++------------ 19 files changed, 257 insertions(+), 378 deletions(-) diff --git a/client/BasinHoppingJob.cpp b/client/BasinHoppingJob.cpp index 98f399a52..e7e334d0c 100644 --- a/client/BasinHoppingJob.cpp +++ b/client/BasinHoppingJob.cpp @@ -10,8 +10,8 @@ ** https://github.com/TheochemUI/eOn */ -#include -#include +#include +#include #include #include "BasinHoppingJob.h" @@ -82,9 +82,7 @@ std::vector BasinHoppingJob::run(void) { *minimumEnergyStructure = *current; int nsteps = params.basin_hopping_options.steps + params.basin_hopping_options.quenching_steps; - long totalfc; - FILE *pFile; - pFile = fopen("bh.dat", "w"); + auto bhFile = fmt::output_file("bh.dat"); SPDLOG_LOGGER_DEBUG( log, "[Basin Hopping] {:4s} {:12s} {:12s} {:12s} {:4s} {:5s} {:5s}", @@ -190,9 +188,10 @@ std::vector BasinHoppingJob::run(void) { snprintf(fname, 128, "energy_%.5i.dat", step + 1); returnFiles.push_back(fname); - FILE *fh = fopen(fname, "w"); - fprintf(fh, "%.10e\n", currentEnergy); - fclose(fh); + { + auto efh = fmt::output_file(fname); + efh.print("{:.10e}\n", currentEnergy); + } } } @@ -205,21 +204,13 @@ std::vector BasinHoppingJob::run(void) { minTrial->matter2con("movie", true); } - // totalfc = Potential::fcallsTotal; - char acceptReject[2]; - acceptReject[1] = '\0'; - if (accepted) { - acceptReject[0] = 'A'; - } else { - acceptReject[0] = 'R'; - } - // SPDLOG_LOGGER_DEBUG(log, "[Basin Hopping] %5i %12.3f %12.3f %12.3f %4i - // %5.3f %5.3f %1s\n", - // step+1, currentEnergy, minTrial->getPotentialEnergy(), - // minimumEnergy, minfcalls, totalAccept/((double)step+1), - // curDisplacement, acceptReject); - // fprintf(pFile, "%6i %9ld %12.4e %12.4e\n",step+1,totalfc,currentEnergy, - // minTrial->getPotentialEnergy()); + SPDLOG_LOGGER_DEBUG( + log, "[Basin Hopping] {:5d} {:12.3f} {:12.3f} {:12.3f} {:5.3f} {:5.3f} {:1s}", + step + 1, currentEnergy, minTrial->getPotentialEnergy(), + minimumEnergy, totalAccept / (static_cast(step) + 1), + curDisplacement, accepted ? "A" : "R"); + bhFile.print("{:6d} {:12.4e} {:12.4e}\n", step + 1, currentEnergy, + minTrial->getPotentialEnergy()); if (minimumEnergy < params.basin_hopping_options.stop_energy) { break; @@ -261,37 +252,34 @@ std::vector BasinHoppingJob::run(void) { recentAccept = 0; } } - fclose(pFile); /* Save Results */ - FILE *fileResults; - std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); - fileResults = fopen(resultsFilename.c_str(), "wb"); + { + auto out = fmt::output_file(resultsFilename); - if (params.debug_options.write_movies == true) { - std::string movieFilename("movie.xyz"); - returnFiles.push_back(movieFilename); - } + if (params.debug_options.write_movies == true) { + std::string movieFilename("movie.xyz"); + returnFiles.push_back(movieFilename); + } - fprintf(fileResults, "%d termination_reason\n", 0); - fprintf(fileResults, "%.6f minimum_energy\n", minimumEnergy); - fprintf(fileResults, "%ld random_seed\n", params.main_options.randomSeed); - fprintf(fileResults, "%.3f acceptance_ratio\n", - totalAccept / params.basin_hopping_options.steps); - if (params.basin_hopping_options.swap_probability > 0) { - fprintf(fileResults, "%.3f swap_acceptance_ratio\n", - swap_accept / double(swap_count)); + out.print("{} termination_reason\n", 0); + out.print("{:.6f} minimum_energy\n", minimumEnergy); + out.print("{} random_seed\n", params.main_options.randomSeed); + out.print("{:.3f} acceptance_ratio\n", + totalAccept / params.basin_hopping_options.steps); + if (params.basin_hopping_options.swap_probability > 0) { + out.print("{:.3f} swap_acceptance_ratio\n", + swap_accept / double(swap_count)); + } + out.print("{} total_normal_displacement_steps\n", + disp_count - jump_count - + params.basin_hopping_options.quenching_steps); + out.print("{} total_jump_steps\n", jump_count); + out.print("{} total_swap_steps\n", swap_count); } - fprintf(fileResults, "%ld total_normal_displacement_steps\n", - disp_count - jump_count - - params.basin_hopping_options.quenching_steps); - fprintf(fileResults, "%d total_jump_steps\n", jump_count); - fprintf(fileResults, "%d total_swap_steps\n", swap_count); - // fprintf(fileResults, "%d total_force_calls\n", Potential::fcallsTotal); - fclose(fileResults); std::string productFilename("min.con"); returnFiles.push_back(productFilename); diff --git a/client/DynamicsJob.cpp b/client/DynamicsJob.cpp index 7170aec93..60fe83fc6 100644 --- a/client/DynamicsJob.cpp +++ b/client/DynamicsJob.cpp @@ -9,7 +9,6 @@ ** Repo: ** https://github.com/TheochemUI/eOn */ -#include #include #include "Dynamics.h" diff --git a/client/FiniteDifferenceJob.cpp b/client/FiniteDifferenceJob.cpp index 2949b32ad..6625fb98d 100644 --- a/client/FiniteDifferenceJob.cpp +++ b/client/FiniteDifferenceJob.cpp @@ -36,10 +36,10 @@ std::vector FiniteDifferenceJob::run(void) { AtomMatrix displacement; displacement.resize(reactant->numberOfAtoms(), 3); displacement.setZero(); - printf("displacing atoms:"); + SPDLOG_DEBUG( "displacing atoms:"); for (int i = 0; i < reactant->numberOfAtoms(); i++) { if (reactant->distance(epicenter, i) <= 3.3) { - printf(" %i", i); + SPDLOG_DEBUG( " {}", i); for (int j = 0; j < 3; j++) { if (!reactant->getFixed(i)) { displacement(i, j) = randomDouble(1.0); @@ -47,13 +47,12 @@ std::vector FiniteDifferenceJob::run(void) { } } } - printf("\n"); displacement.normalize(); // Loop over values of dimer dR and print the output to results.dat. - FILE *results = fopen("results.dat", "w"); - fprintf(results, "%14s %14s\n", "dR", "curvature"); - printf("%14s %14s\n", "dR", "curvature"); + auto results = fmt::output_file("results.dat"); + results.print("{:>14s} {:>14s}\n", "dR", "curvature"); + SPDLOG_DEBUG( "{:>14s} {:>14s}", "dR", "curvature"); AtomMatrix posB; AtomMatrix forceB; double curvature = 0.0; @@ -63,11 +62,9 @@ std::vector FiniteDifferenceJob::run(void) { forceB = reactant->getForces(); curvature = ((forceB - forceA).array() * displacement.array()).sum() / dRs[dRi]; - fprintf(results, "%14.8f %14.8f\n", dRs[dRi], curvature); - printf("%14.8f %14.8f\n", dRs[dRi], curvature); - fflush(results); + results.print("{:14.8f} {:14.8f}\n", dRs[dRi], curvature); + SPDLOG_DEBUG( "{:14.8f} {:14.8f}", dRs[dRi], curvature); } - fclose(results); std::vector empty; return empty; diff --git a/client/GlobalOptimizationJob.cpp b/client/GlobalOptimizationJob.cpp index cbf46b6e2..352d6969e 100644 --- a/client/GlobalOptimizationJob.cpp +++ b/client/GlobalOptimizationJob.cpp @@ -72,8 +72,8 @@ std::vector GlobalOptimizationJob::run(void) { } else { earrim1 = earr[i - 1]; } - fprintf(earrfile, "%5zu %15.5f %15.5f %15.5f ", i + 1, earr[i], - earr[i] - earr[0], earr[i] - earrim1); + earrfile.print("{:5d} {:15.5f} {:15.5f} {:15.5f} ", i + 1, earr[i], + earr[i] - earr[0], earr[i] - earrim1); } // globopt.run(); return returnFiles; @@ -191,8 +191,8 @@ void GlobalOptimizationJob::report(Matter *matter_hop) { double epot_hop = matter_hop->getPotentialEnergy(); double temp = (2.0 * ekin_p / params.constants.kB); double dt = params.dynamics_options.time_step; - fprintf(monfile, "%15.5f %15.5f %11zu %12.2f %c%c %5ld %5ld", - epot_hop, ediff, (size_t)temp, dt, C1, C2, fcallsMove, fcallsRelax); + monfile.print("{:15.5f} {:15.5f} {:11d} {:12.2f} {:c}{:c} {:5d} {:5d}", + epot_hop, ediff, static_cast(temp), dt, C1, C2, fcallsMove, fcallsRelax); } void GlobalOptimizationJob::decisionStep(Matter *matter_cur, diff --git a/client/GlobalOptimizationJob.h b/client/GlobalOptimizationJob.h index fd68b6b22..e7ac3dd5d 100644 --- a/client/GlobalOptimizationJob.h +++ b/client/GlobalOptimizationJob.h @@ -14,6 +14,8 @@ #include "Matter.h" #include "Parameters.h" +#include + class GlobalOptimizationJob : public Job { public: GlobalOptimizationJob(std::unique_ptr parameters) @@ -30,17 +32,12 @@ class GlobalOptimizationJob : public Job { fcallsMove{0}, firstStep{true}, fcallsRelax{0}, - monfile{fopen("monitoring.dat", "w")}, - earrfile{fopen("earr.dat", "w")} { + monfile{fmt::output_file("monitoring.dat")}, + earrfile{fmt::output_file("earr.dat")} { log = spdlog::get("combi"); } - // etoler = parameters->globalOptimizationEtoler; - // decisionMethod = "NPEW"; - ~GlobalOptimizationJob(void) { - fclose(monfile); - fclose(earrfile); - }; + ~GlobalOptimizationJob(void) = default; void hoppingStep(long, Matter *, Matter *); void decisionStep(Matter *, Matter *); void report(Matter *); @@ -76,7 +73,7 @@ class GlobalOptimizationJob : public Job { // string decisionMethod; string decisionResult; string hoppingResult; - FILE *monfile; - FILE *earrfile; + fmt::ostream monfile; + fmt::ostream earrfile; std::shared_ptr log; }; diff --git a/client/HelperFunctions.cpp b/client/HelperFunctions.cpp index 2e68e4137..bc354bf82 100644 --- a/client/HelperFunctions.cpp +++ b/client/HelperFunctions.cpp @@ -615,17 +615,18 @@ AtomMatrix helper_functions::loadMode(string filename, int nAtoms) { return mode; } -void helper_functions::saveMode(FILE *modeFile, std::shared_ptr matter, +void helper_functions::saveMode(const std::string &filename, + std::shared_ptr matter, AtomMatrix mode) { + auto out = fmt::output_file(filename); long const nAtoms = matter->numberOfAtoms(); for (long i = 0; i < nAtoms; ++i) { if (matter->getFixed(i)) { - fprintf(modeFile, "0 0 0\n"); + out.print("0 0 0\n"); } else { - fprintf(modeFile, "%lf\t%lf \t%lf\n", mode(i, 0), mode(i, 1), mode(i, 2)); + out.print("{:f}\t{:f} \t{:f}\n", mode(i, 0), mode(i, 1), mode(i, 2)); } } - return; } std::vector helper_functions::split_string_int(std::string s, diff --git a/client/HelperFunctions.h b/client/HelperFunctions.h index e9208e4da..b21c97940 100644 --- a/client/HelperFunctions.h +++ b/client/HelperFunctions.h @@ -89,7 +89,8 @@ getRelevantFile(string filename); // return filename containing _checkpoint or VectorXd loadMasses(string filename, int nAtoms); AtomMatrix loadMode(FILE *modeFile, int nAtoms); AtomMatrix loadMode(string filename, int nAtoms); -void saveMode(FILE *modeFile, std::shared_ptr matter, AtomMatrix mode); +void saveMode(const std::string &filename, std::shared_ptr matter, + AtomMatrix mode); std::vector split_string_int(std::string s, std::string delim); bool identical(const Matter &m1, const Matter &m2, diff --git a/client/HessianJob.cpp b/client/HessianJob.cpp index 395885b06..3bcad9a79 100644 --- a/client/HessianJob.cpp +++ b/client/HessianJob.cpp @@ -39,17 +39,12 @@ std::vector HessianJob::run(void) { moved = moved.head(nMoved); hessian.getFreqs(matter.get(), moved); - FILE *fileResults; - // FILE *fileMode; - std::string results_file("results.dat"); - returnFiles.push_back(results_file); - - fileResults = fopen(results_file.c_str(), "wb"); - - // fprintf(fileResults, "%d force_calls\n", Potential::fcalls); - fclose(fileResults); + { + // Create empty results file + auto out = fmt::output_file(results_file); + } return returnFiles; } diff --git a/client/MinModeSaddleSearch.cpp b/client/MinModeSaddleSearch.cpp index aa61988fa..daac55643 100644 --- a/client/MinModeSaddleSearch.cpp +++ b/client/MinModeSaddleSearch.cpp @@ -441,10 +441,8 @@ int MinModeSaddleSearch::run() { if (params.main_options.checkpoint) { matter->matter2con("displacement_cp.con", false); - FILE *fileMode = fopen("mode_cp.dat", "wb"); - helper_functions::saveMode(fileMode, matter, + helper_functions::saveMode("mode_cp.dat", matter, minModeMethod->getEigenvector()); - fclose(fileMode); } if (de > params.saddle_search_options.max_energy) { diff --git a/client/MinimizationJob.cpp b/client/MinimizationJob.cpp index b0eccd286..b6883eb99 100644 --- a/client/MinimizationJob.cpp +++ b/client/MinimizationJob.cpp @@ -25,9 +25,7 @@ std::vector MinimizationJob::run(void) { string posOutFilename("min.con"); if (params.main_options.checkpoint) { - FILE *pos_file; - pos_file = fopen("pos_cp.con", "r"); - if (pos_file != NULL) { + if (std::filesystem::exists("pos_cp.con")) { posInFilename = "pos_cp.con"; SPDLOG_LOGGER_DEBUG(log, "[Minimization] Resuming from checkpoint"); } else { diff --git a/client/MonteCarloJob.cpp b/client/MonteCarloJob.cpp index d36437775..5bb0dd239 100644 --- a/client/MonteCarloJob.cpp +++ b/client/MonteCarloJob.cpp @@ -14,14 +14,14 @@ #include "Matter.h" #include "MonteCarlo.h" +#include + std::vector MonteCarloJob::run(void) { string posInFilename("pos.con"); string posOutFilename("out.con"); if (params.main_options.checkpoint) { - FILE *pos; - pos = fopen("pos_cp.con", "r"); - if (pos != NULL) { + if (std::filesystem::exists("pos_cp.con")) { posInFilename = "pos_cp.con"; SPDLOG_LOGGER_DEBUG(log, "Resuming from checkpoint\n"); } else { @@ -40,22 +40,8 @@ std::vector MonteCarloJob::run(void) { mc.run(params.monte_carlo_options.steps, params.main_options.temperature, params.monte_carlo_options.step_size); - // FILE *fileResults; - std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); - // fileResults = fopen(resultsFilename.c_str(), "wb"); - - // fprintf(fileResults, "%d termination_reason\n", status); - // fprintf(fileResults, "minimization job_type\n"); - // fprintf(fileResults, "%s potential_type\n", - // helper_functions::getPotentialName(params.potential_options.potential).c_str()); - // fprintf(fileResults, "%d total_force_calls\n", Potential::fcallsTotal); - // if (status != STATUS_POTENTIAL_FAILED) { - // fprintf(fileResults, "%f potential_energy\n", - // pos->getPotentialEnergy()); - // } - // fclose(fileResults); return returnFiles; } diff --git a/client/NudgedElasticBandJob.cpp b/client/NudgedElasticBandJob.cpp index 1ba2668d7..1d21cd640 100644 --- a/client/NudgedElasticBandJob.cpp +++ b/client/NudgedElasticBandJob.cpp @@ -14,6 +14,8 @@ #include "NEBInitialPaths.hpp" #include "Potential.h" +#include + using namespace std; std::vector NudgedElasticBandJob::run(void) { @@ -26,10 +28,8 @@ std::vector NudgedElasticBandJob::run(void) { string transitionStateFilename = helper_functions::getRelevantFile("ts.con"); bool tsInterpolate = false; auto transitionState = std::make_shared(pot, params); - FILE *fhTransitionState = fopen("ts.con", "r"); - if (fhTransitionState != nullptr) { + if (std::filesystem::exists("ts.con")) { tsInterpolate = true; - fclose(fhTransitionState); transitionState->con2matter(transitionStateFilename); } else { transitionState = nullptr; @@ -135,49 +135,37 @@ std::vector NudgedElasticBandJob::run(void) { void NudgedElasticBandJob::saveData(NudgedElasticBand::NEBStatus status, NudgedElasticBand *neb) { - FILE *fileResults; - std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); - fileResults = fopen(resultsFilename.c_str(), "wb"); - if (!fileResults) { - SPDLOG_LOGGER_ERROR(m_log, "Failed to open {} for writing", - resultsFilename); - return; - } - - fprintf(fileResults, "%d termination_reason\n", static_cast(status)); - fprintf(fileResults, "%s potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)} - .c_str()); - // fprintf(fileResults, "%ld total_force_calls\n", Potential::fcalls); - // fprintf(fileResults, "%ld force_calls_neb\n", fCallsNEB); - fprintf(fileResults, "%f energy_reference\n", - neb->path[0]->getPotentialEnergy()); - fprintf(fileResults, "%li number_of_images\n", neb->numImages); - - for (long i = 0; i <= neb->numImages + 1; i++) { - fprintf(fileResults, "%f image%li_energy\n", - neb->path[i]->getPotentialEnergy() - - neb->path[0]->getPotentialEnergy(), - i); - fprintf(fileResults, "%f image%li_force\n", - neb->path[i]->getForces().norm(), i); - - // Only interior images have a meaningful projected force - double proj_norm = - (i >= 1 && i <= neb->numImages) ? neb->projectedForce[i]->norm() : 0.0; - fprintf(fileResults, "%f image%li_projected_force\n", proj_norm, i); - } + { + auto out = fmt::output_file(resultsFilename); + out.print("{} termination_reason\n", static_cast(status)); + out.print("{} potential_type\n", + std::string{magic_enum::enum_name( + params.potential_options.potential)}); + out.print("{:f} energy_reference\n", neb->path[0]->getPotentialEnergy()); + out.print("{} number_of_images\n", neb->numImages); + + for (long i = 0; i <= neb->numImages + 1; i++) { + out.print("{:f} image{}_energy\n", + neb->path[i]->getPotentialEnergy() - + neb->path[0]->getPotentialEnergy(), + i); + out.print("{:f} image{}_force\n", neb->path[i]->getForces().norm(), i); + + double proj_norm = + (i >= 1 && i <= neb->numImages) + ? neb->projectedForce[i]->norm() + : 0.0; + out.print("{:f} image{}_projected_force\n", proj_norm, i); + } - fprintf(fileResults, "%li number_of_extrema\n", neb->numExtrema); - for (long i = 0; i < neb->numExtrema; i++) { - fprintf(fileResults, "%f extremum%li_position\n", neb->extremumPosition[i], - i); - fprintf(fileResults, "%f extremum%li_energy\n", neb->extremumEnergy[i], i); + out.print("{} number_of_extrema\n", neb->numExtrema); + for (long i = 0; i < neb->numExtrema; i++) { + out.print("{:f} extremum{}_position\n", neb->extremumPosition[i], i); + out.print("{:f} extremum{}_energy\n", neb->extremumEnergy[i], i); + } } - fclose(fileResults); // Save the Full NEB Path std::string nebFilename("neb.con"); @@ -224,15 +212,14 @@ void NudgedElasticBandJob::saveData(NudgedElasticBand::NEBStatus status, std::string peakModeFile = fmt::format("peak{:02d}_mode.dat", peakCount); - FILE *fMode = fopen(peakModeFile.c_str(), "w"); - if (fMode) { + { + auto modeOut = fmt::output_file(peakModeFile); for (int row = 0; row < peakMode.rows(); ++row) { - fprintf(fMode, "%12.6f %12.6f %12.6f\n", peakMode(row, 0), - peakMode(row, 1), peakMode(row, 2)); + modeOut.print("{:12.6f} {:12.6f} {:12.6f}\n", peakMode(row, 0), + peakMode(row, 1), peakMode(row, 2)); } - fclose(fMode); - returnFiles.push_back(peakModeFile); } + returnFiles.push_back(peakModeFile); SPDLOG_LOGGER_INFO( m_log, diff --git a/client/ParallelReplicaJob.cpp b/client/ParallelReplicaJob.cpp index 62844250b..d81f681dd 100644 --- a/client/ParallelReplicaJob.cpp +++ b/client/ParallelReplicaJob.cpp @@ -199,39 +199,35 @@ std::vector ParallelReplicaJob::run(void) { product.matter2con("product.con"); // report the results - FILE *fileResults; std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); - fileResults = fopen(resultsFilename.c_str(), "wb"); - fprintf(fileResults, "%s potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)} - .c_str()); - fprintf(fileResults, "%ld random_seed\n", params.main_options.randomSeed); - fprintf(fileResults, "%f potential_energy_reactant\n", - reactant->getPotentialEnergy()); - // fprintf(fileResults, "%i force_calls_refine\n", refineForceCalls); - // fprintf(fileResults, "%d total_force_calls\n", Potential::fcalls); - - if (transitionTime == 0) { - fprintf(fileResults, "0 transition_found\n"); - fprintf(fileResults, "%e simulation_time_s\n", - simulationTime * params.constants.timeUnit * 1.0e-15); - } else { - fprintf(fileResults, "1 transition_found\n"); - fprintf(fileResults, "%e transition_time_s\n", - transitionTime * params.constants.timeUnit * 1.0e-15); - fprintf(fileResults, "%e correlation_time_s\n", - params.parallel_replica_options.corr_time * - params.constants.timeUnit * 1.0e-15); - fprintf(fileResults, "%lf potential_energy_product\n", - product.getPotentialEnergy()); + { + auto out = fmt::output_file(resultsFilename); + out.print("{} potential_type\n", + std::string{magic_enum::enum_name( + params.potential_options.potential)}); + out.print("{} random_seed\n", params.main_options.randomSeed); + out.print("{:f} potential_energy_reactant\n", + reactant->getPotentialEnergy()); + + if (transitionTime == 0) { + out.print("0 transition_found\n"); + out.print("{:e} simulation_time_s\n", + simulationTime * params.constants.timeUnit * 1.0e-15); + } else { + out.print("1 transition_found\n"); + out.print("{:e} transition_time_s\n", + transitionTime * params.constants.timeUnit * 1.0e-15); + out.print("{:e} correlation_time_s\n", + params.parallel_replica_options.corr_time * + params.constants.timeUnit * 1.0e-15); + out.print("{:f} potential_energy_product\n", + product.getPotentialEnergy()); + } + out.print("{:f} speedup\n", + simulationTime / (params.dynamics_options.steps * + params.dynamics_options.time_step)); } - fprintf(fileResults, "%lf speedup\n", - simulationTime / (params.dynamics_options.steps * - params.dynamics_options.time_step)); - - fclose(fileResults); MDSnapshots.clear(); MDTimes.clear(); diff --git a/client/PrefactorJob.cpp b/client/PrefactorJob.cpp index 0845c4142..a35b6c8ad 100644 --- a/client/PrefactorJob.cpp +++ b/client/PrefactorJob.cpp @@ -89,29 +89,26 @@ std::vector PrefactorJob::run(void) { bool failed = freqs.size() != 3 * atoms.rows(); - FILE *fileResults; - FILE *fileFreq; - std::string results_file("results.dat"); std::string freq_file("freq.dat"); returnFiles.push_back(results_file); returnFiles.push_back(freq_file); - fileResults = fopen(results_file.c_str(), "wb"); - fileFreq = fopen(freq_file.c_str(), "wb"); - - fprintf(fileResults, "%s good\n", failed ? "false" : "true"); - // fprintf(fileResults, "%d force_calls\n", Potential::fcalls); + { + auto out = fmt::output_file(results_file); + out.print("{} good\n", failed ? "false" : "true"); + } if (!failed) { + auto fout = fmt::output_file(freq_file); for (int i = 0; i < freqs.size(); i++) { if (0. < freqs[i]) { - fprintf(fileFreq, "%f\n", - sqrt(freqs[i]) / (2 * helper_functions::pi * 10.18e-15)); + fout.print("{:f}\n", + sqrt(freqs[i]) / (2 * helper_functions::pi * 10.18e-15)); } else { - fprintf(fileFreq, "%f\n", - -sqrt(-freqs[i]) / (2 * helper_functions::pi * 10.18e-15)); + fout.print("{:f}\n", + -sqrt(-freqs[i]) / (2 * helper_functions::pi * 10.18e-15)); } } } diff --git a/client/ProcessSearchJob.cpp b/client/ProcessSearchJob.cpp index 3489f8c66..a5d034aa5 100644 --- a/client/ProcessSearchJob.cpp +++ b/client/ProcessSearchJob.cpp @@ -235,56 +235,44 @@ int ProcessSearchJob::doProcessSearch(void) { } void ProcessSearchJob::saveData(int status) { - FILE *fileResults, *fileMode; - std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); - fileResults = fopen(resultsFilename.c_str(), "wb"); - // XXX: min_fcalls isn't quite right it should get them from - // the minimizer. But right now the minimizers are in - // the SaddleSearch object. They will be taken out eventually. - - fprintf(fileResults, "%d termination_reason\n", status); - fprintf(fileResults, "%ld random_seed\n", params.main_options.randomSeed); - fprintf(fileResults, "%s potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)} - .c_str()); - fprintf(fileResults, "%zu total_force_calls\n", - fCallsMin + fCallsSaddle + fCallsPrefactors); - fprintf(fileResults, "%zu force_calls_minimization\n", fCallsMin); - // fprintf(fileResults, "%ld force_calls_minimization\n", - // SaddleSearch->forceCallsMinimization + fCallsMin); - fprintf(fileResults, "%zu force_calls_saddle\n", fCallsSaddle); - fprintf(fileResults, "%.12e potential_energy_saddle\n", - saddle->getPotentialEnergy()); - fprintf(fileResults, "%.12e potential_energy_reactant\n", - min1->getPotentialEnergy()); - fprintf(fileResults, "%.12e potential_energy_product\n", - min2->getPotentialEnergy()); - fprintf(fileResults, "%.12e barrier_reactant_to_product\n", - barriersValues[0]); - fprintf(fileResults, "%.12e barrier_product_to_reactant\n", - barriersValues[1]); - if (params.saddle_search_options.method == "min_mode") { - fprintf(fileResults, "%.12e displacement_saddle_distance\n", - displacement->perAtomNorm(*saddle)); - } else { - fprintf(fileResults, "%.12e displacement_saddle_distance\n", 0.0); - } - if (params.saddle_search_options.method == "dynamics") { - auto ds = dynamic_cast(*saddleSearch); - fprintf(fileResults, "%.12e simulation_time\n", - ds.time * params.constants.timeUnit); - fprintf(fileResults, "%.12e md_temperature\n", - params.saddle_search_options.dynamics.temperature); + { + auto out = fmt::output_file(resultsFilename); + out.print("{} termination_reason\n", status); + out.print("{} random_seed\n", params.main_options.randomSeed); + out.print("{} potential_type\n", + std::string{magic_enum::enum_name( + params.potential_options.potential)}); + out.print("{} total_force_calls\n", + fCallsMin + fCallsSaddle + fCallsPrefactors); + out.print("{} force_calls_minimization\n", fCallsMin); + out.print("{} force_calls_saddle\n", fCallsSaddle); + out.print("{:.12e} potential_energy_saddle\n", + saddle->getPotentialEnergy()); + out.print("{:.12e} potential_energy_reactant\n", + min1->getPotentialEnergy()); + out.print("{:.12e} potential_energy_product\n", + min2->getPotentialEnergy()); + out.print("{:.12e} barrier_reactant_to_product\n", barriersValues[0]); + out.print("{:.12e} barrier_product_to_reactant\n", barriersValues[1]); + if (params.saddle_search_options.method == "min_mode") { + out.print("{:.12e} displacement_saddle_distance\n", + displacement->perAtomNorm(*saddle)); + } else { + out.print("{:.12e} displacement_saddle_distance\n", 0.0); + } + if (params.saddle_search_options.method == "dynamics") { + auto ds = dynamic_cast(*saddleSearch); + out.print("{:.12e} simulation_time\n", + ds.time * params.constants.timeUnit); + out.print("{:.12e} md_temperature\n", + params.saddle_search_options.dynamics.temperature); + } + out.print("{} force_calls_prefactors\n", fCallsPrefactors); + out.print("{:.12e} prefactor_reactant_to_product\n", prefactorsValues[0]); + out.print("{:.12e} prefactor_product_to_reactant\n", prefactorsValues[1]); } - fprintf(fileResults, "%zu force_calls_prefactors\n", fCallsPrefactors); - fprintf(fileResults, "%.12e prefactor_reactant_to_product\n", - prefactorsValues[0]); - fprintf(fileResults, "%.12e prefactor_product_to_reactant\n", - prefactorsValues[1]); - fclose(fileResults); std::string reactantFilename("reactant.con"); returnFiles.push_back(reactantFilename); @@ -292,9 +280,7 @@ void ProcessSearchJob::saveData(int status) { std::string modeFilename("mode.dat"); returnFiles.push_back(modeFilename); - fileMode = fopen(modeFilename.c_str(), "wb"); - helper_functions::saveMode(fileMode, saddle, saddleSearch->getEigenvector()); - fclose(fileMode); + helper_functions::saveMode(modeFilename, saddle, saddleSearch->getEigenvector()); std::string saddleFilename("saddle.con"); returnFiles.push_back(saddleFilename); diff --git a/client/ReplicaExchangeJob.cpp b/client/ReplicaExchangeJob.cpp index d3b6134be..adb762325 100644 --- a/client/ReplicaExchangeJob.cpp +++ b/client/ReplicaExchangeJob.cpp @@ -132,25 +132,20 @@ std::vector ReplicaExchangeJob::run(void) { } void ReplicaExchangeJob::saveData(void) { - - FILE *fileResults, *filePos; - std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); - fileResults = fopen(resultsFilename.c_str(), "wb"); - - fprintf(fileResults, "%ld random_seed\n", params.main_options.randomSeed); - fprintf(fileResults, "%s potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)} - .c_str()); - // fprintf(fileResults, "%ld force_calls_sampling\n", forceCalls); - fclose(fileResults); + { + auto out = fmt::output_file(resultsFilename); + out.print("{} random_seed\n", params.main_options.randomSeed); + out.print("{} potential_type\n", + std::string{magic_enum::enum_name( + params.potential_options.potential)}); + } std::string posFilename("pos_out.con"); returnFiles.push_back(posFilename); - filePos = fopen(posFilename.c_str(), "wb"); - fclose(filePos); - - return; + { + // Create empty pos_out.con + auto out = fmt::output_file(posFilename); + } } diff --git a/client/SaddleSearchJob.cpp b/client/SaddleSearchJob.cpp index 3896a7d41..e2442a6b7 100644 --- a/client/SaddleSearchJob.cpp +++ b/client/SaddleSearchJob.cpp @@ -14,7 +14,7 @@ #include "HelperFunctions.h" #include "Potential.h" -#include +#include #include using namespace std; @@ -25,10 +25,8 @@ std::vector SaddleSearchJob::run(void) { string modeFilename("direction.dat"); if (params.main_options.checkpoint) { - FILE *disp, *mode; - disp = fopen("displacement_cp.con", "r"); - mode = fopen("mode_cp.dat", "r"); - if (disp != NULL && mode != NULL) { + namespace fs = std::filesystem; + if (fs::exists("displacement_cp.con") && fs::exists("mode_cp.dat")) { displacementFilename = "displacement_cp.con"; modeFilename = "mode_cp.dat"; SPDLOG_LOGGER_DEBUG(log, "Resuming from checkpoint"); @@ -96,49 +94,31 @@ int SaddleSearchJob::doSaddleSearch() { } void SaddleSearchJob::saveData(int status) { - FILE *fileResults, *fileMode; - std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); - fileResults = fopen(resultsFilename.c_str(), "wb"); - /// XXX: min_fcalls isn't quite right it should get them from - // the minimizer. But right now the minimizers are in - // the SaddleSearch object. They will be taken out eventually. - - fprintf(fileResults, "%d termination_reason\n", status); - fprintf(fileResults, "saddle_search job_type\n"); - fprintf(fileResults, "%ld random_seed\n", params.main_options.randomSeed); - fprintf(fileResults, "%s potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)} - .c_str()); - if (params.saddle_search_options.minmode_method == - LowestEigenmode::MINMODE_GPRDIMER) { - fprintf(fileResults, "%zu total_force_calls\n", - this->pot->forceCallCounter); - fprintf(fileResults, "%d force_calls_saddle\n", fCallsSaddle); - fprintf(fileResults, "%i iterations\n", saddleSearch->iteration); - } else { - fprintf(fileResults, "%zu total_force_calls\n", - this->pot->forceCallCounter); - fprintf(fileResults, "%d force_calls_saddle\n", fCallsSaddle); - fprintf(fileResults, "%i iterations\n", saddleSearch->iteration); - } - if (status != MinModeSaddleSearch::STATUS_POTENTIAL_FAILED) { - fprintf(fileResults, "%f potential_energy_saddle\n", - saddle->getPotentialEnergy()); - fprintf(fileResults, "%f final_eigenvalue\n", - saddleSearch->getEigenvalue()); + { + auto out = fmt::output_file(resultsFilename); + out.print("{} termination_reason\n", status); + out.print("saddle_search job_type\n"); + out.print("{} random_seed\n", params.main_options.randomSeed); + out.print("{} potential_type\n", + std::string{magic_enum::enum_name( + params.potential_options.potential)}); + out.print("{} total_force_calls\n", this->pot->forceCallCounter); + out.print("{} force_calls_saddle\n", fCallsSaddle); + out.print("{} iterations\n", saddleSearch->iteration); + if (status != MinModeSaddleSearch::STATUS_POTENTIAL_FAILED) { + out.print("{:f} potential_energy_saddle\n", + saddle->getPotentialEnergy()); + out.print("{:f} final_eigenvalue\n", saddleSearch->getEigenvalue()); + } + out.print("{:f} potential_energy_reactant\n", + initial->getPotentialEnergy()); } - fprintf(fileResults, "%f potential_energy_reactant\n", - initial->getPotentialEnergy()); - fclose(fileResults); std::string modeFilename("mode.dat"); returnFiles.push_back(modeFilename); - fileMode = fopen(modeFilename.c_str(), "wb"); - helper_functions::saveMode(fileMode, saddle, saddleSearch->getEigenvector()); - fclose(fileMode); + helper_functions::saveMode(modeFilename, saddle, saddleSearch->getEigenvector()); std::string saddleFilename("saddle.con"); returnFiles.push_back(saddleFilename); diff --git a/client/SafeHyperJob.cpp b/client/SafeHyperJob.cpp index f250a5055..026a16902 100644 --- a/client/SafeHyperJob.cpp +++ b/client/SafeHyperJob.cpp @@ -286,48 +286,37 @@ int SafeHyperJob::dynamics() { } void SafeHyperJob::saveData(int status) { - FILE *fileResults; - std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); - fileResults = fopen(resultsFilename.c_str(), "wb"); - // long totalFCalls = minimizeFCalls + mdFCalls + dephaseFCalls + - // refineFCalls; - - fprintf(fileResults, "%s potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)} - .c_str()); - fprintf(fileResults, "%ld random_seed\n", params.main_options.randomSeed); - fprintf(fileResults, "%lf potential_energy_reactant\n", - reactant->getPotentialEnergy()); - // fprintf(fileResults, "%ld total_force_calls\n", totalFCalls); - fprintf(fileResults, "%ld force_calls_dephase\n", dephaseFCalls); - fprintf(fileResults, "%ld force_calls_dynamics\n", mdFCalls); - fprintf(fileResults, "%ld force_calls_minimize\n", minimizeFCalls); - // fprintf(fileResults, "%ld force_calls_refine\n", refineFCalls); - - // fprintf(fileResults, "%d termination_reason\n", status); - fprintf(fileResults, "%d transition_found\n", (newStateFlag) ? 1 : 0); + { + auto out = fmt::output_file(resultsFilename); + out.print("{} potential_type\n", + std::string{magic_enum::enum_name( + params.potential_options.potential)}); + out.print("{} random_seed\n", params.main_options.randomSeed); + out.print("{:f} potential_energy_reactant\n", + reactant->getPotentialEnergy()); + out.print("{} force_calls_dephase\n", dephaseFCalls); + out.print("{} force_calls_dynamics\n", mdFCalls); + out.print("{} force_calls_minimize\n", minimizeFCalls); + out.print("{} transition_found\n", (newStateFlag) ? 1 : 0); + + if (newStateFlag) { + out.print("{:e} transition_time_s\n", + minCorrectedTime * 1.0e-15 * params.constants.timeUnit); + out.print("{:f} potential_energy_product\n", + product->getPotentialEnergy()); + out.print("{:f} moved_distance\n", product->distanceTo(*reactant)); + } - if (newStateFlag) { - fprintf(fileResults, "%e transition_time_s\n", - minCorrectedTime * 1.0e-15 * params.constants.timeUnit); - fprintf(fileResults, "%lf potential_energy_product\n", - product->getPotentialEnergy()); - fprintf(fileResults, "%lf moved_distance\n", - product->distanceTo(*reactant)); + out.print("{:e} simulation_time_s\n", + time * 1.0e-15 * params.constants.timeUnit); + out.print("{:f} speedup\n", + time / params.dynamics_options.steps / + params.dynamics_options.time_step); } - fprintf(fileResults, "%e simulation_time_s\n", - time * 1.0e-15 * params.constants.timeUnit); - fprintf(fileResults, "%lf speedup\n", - time / params.dynamics_options.steps / - params.dynamics_options.time_step); - - fclose(fileResults); - std::string reactantFilename("reactant.con"); returnFiles.push_back(reactantFilename); reactant->matter2con(reactantFilename); diff --git a/client/TADJob.cpp b/client/TADJob.cpp index 9930b551a..bf901a542 100644 --- a/client/TADJob.cpp +++ b/client/TADJob.cpp @@ -276,48 +276,37 @@ int TADJob::dynamics() { } void TADJob::saveData(int status) { - FILE *fileResults; - std::string resultsFilename("results.dat"); returnFiles.push_back(resultsFilename); - fileResults = fopen(resultsFilename.c_str(), "wb"); - // long totalFCalls = minimizeFCalls + mdFCalls + dephaseFCalls + - // refineFCalls; - - fprintf(fileResults, "%s potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)} - .c_str()); - fprintf(fileResults, "%ld random_seed\n", params.main_options.randomSeed); - fprintf(fileResults, "%lf potential_energy_reactant\n", - reactant->getPotentialEnergy()); - // fprintf(fileResults, "%ld total_force_calls\n", totalFCalls); - // fprintf(fileResults, "%ld force_calls_dephase\n", dephaseFCalls); - fprintf(fileResults, "%ld force_calls_dynamics\n", mdFCalls); - fprintf(fileResults, "%ld force_calls_minimize\n", minimizeFCalls); - fprintf(fileResults, "%ld force_calls_refine\n", refineFCalls); - - // fprintf(fileResults, "%d termination_reason\n", status); - fprintf(fileResults, "%d transition_found\n", (newStateFlag) ? 1 : 0); + { + auto out = fmt::output_file(resultsFilename); + out.print("{} potential_type\n", + std::string{magic_enum::enum_name( + params.potential_options.potential)}); + out.print("{} random_seed\n", params.main_options.randomSeed); + out.print("{:f} potential_energy_reactant\n", + reactant->getPotentialEnergy()); + out.print("{} force_calls_dynamics\n", mdFCalls); + out.print("{} force_calls_minimize\n", minimizeFCalls); + out.print("{} force_calls_refine\n", refineFCalls); + out.print("{} transition_found\n", (newStateFlag) ? 1 : 0); + + if (newStateFlag) { + out.print("{:e} transition_time_s\n", + minCorrectedTime * 1.0e-15 * params.constants.timeUnit); + out.print("{:f} potential_energy_product\n", + product->getPotentialEnergy()); + out.print("{:f} moved_distance\n", product->distanceTo(*reactant)); + } - if (newStateFlag) { - fprintf(fileResults, "%e transition_time_s\n", - minCorrectedTime * 1.0e-15 * params.constants.timeUnit); - fprintf(fileResults, "%lf potential_energy_product\n", - product->getPotentialEnergy()); - fprintf(fileResults, "%lf moved_distance\n", - product->distanceTo(*reactant)); + out.print("{:e} simulation_time_s\n", + time * 1.0e-15 * params.constants.timeUnit); + out.print("{:f} speedup\n", + time / params.dynamics_options.steps / + params.dynamics_options.time_step); } - fprintf(fileResults, "%e simulation_time_s\n", - time * 1.0e-15 * params.constants.timeUnit); - fprintf(fileResults, "%lf speedup\n", - time / params.dynamics_options.steps / - params.dynamics_options.time_step); - - fclose(fileResults); - std::string reactantFilename("reactant.con"); returnFiles.push_back(reactantFilename); reactant->matter2con(reactantFilename); From 48c48553437afcbc823eddea55faac21080fe104 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 12:28:25 +0100 Subject: [PATCH 05/22] ci(chore): fixup --- .github/workflows/ci_benchmark.yml | 2 +- .github/workflows/ci_build_akmc.yml | 2 +- .github/workflows/ci_build_gprd.yml | 2 +- .github/workflows/ci_docs.yml | 2 +- .github/workflows/ci_metatomic.yml | 2 +- .github/workflows/ci_serve.yml | 2 +- .github/workflows/ci_xtb.yml | 2 +- pixi.lock | 5776 ++++++++++++++++++++------- 8 files changed, 4424 insertions(+), 1366 deletions(-) diff --git a/.github/workflows/ci_benchmark.yml b/.github/workflows/ci_benchmark.yml index 0bc21ef30..781182d8a 100644 --- a/.github/workflows/ci_benchmark.yml +++ b/.github/workflows/ci_benchmark.yml @@ -35,7 +35,7 @@ jobs: cp -r /tmp/_bench_preserve/benchmarks/ benchmarks/ cp /tmp/_bench_preserve/asv.conf.json asv.conf.json - - uses: prefix-dev/setup-pixi@v0.8.10 + - uses: prefix-dev/setup-pixi@v0.9.4 with: cache: true cache-write: false diff --git a/.github/workflows/ci_build_akmc.yml b/.github/workflows/ci_build_akmc.yml index 1335898bf..500f35d86 100644 --- a/.github/workflows/ci_build_akmc.yml +++ b/.github/workflows/ci_build_akmc.yml @@ -17,7 +17,7 @@ jobs: os: [ubuntu-22.04, macos-14, windows-latest] steps: - uses: actions/checkout@v4 - - uses: prefix-dev/setup-pixi@v0.8.10 + - uses: prefix-dev/setup-pixi@v0.9.4 with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} diff --git a/.github/workflows/ci_build_gprd.yml b/.github/workflows/ci_build_gprd.yml index 7b4bededf..2cc39da23 100644 --- a/.github/workflows/ci_build_gprd.yml +++ b/.github/workflows/ci_build_gprd.yml @@ -24,7 +24,7 @@ jobs: git clone git@github.com:TheochemUI/gpr_optim.git subprojects/gpr_optim cd subprojects/gpr_optim git checkout 26242c8e94569ef81103ece4662008c3250ada55 - - uses: prefix-dev/setup-pixi@v0.8.10 + - uses: prefix-dev/setup-pixi@v0.9.4 with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml index 10c5b30de..c87827411 100644 --- a/.github/workflows/ci_docs.yml +++ b/.github/workflows/ci_docs.yml @@ -25,7 +25,7 @@ jobs: with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@v0.8.10 + - uses: prefix-dev/setup-pixi@v0.9.4 with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} diff --git a/.github/workflows/ci_metatomic.yml b/.github/workflows/ci_metatomic.yml index 2f613d723..42f463973 100644 --- a/.github/workflows/ci_metatomic.yml +++ b/.github/workflows/ci_metatomic.yml @@ -18,7 +18,7 @@ jobs: os: [ubuntu-22.04, macos-14] steps: - uses: actions/checkout@v4 - - uses: prefix-dev/setup-pixi@v0.8.10 + - uses: prefix-dev/setup-pixi@v0.9.4 with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} diff --git a/.github/workflows/ci_serve.yml b/.github/workflows/ci_serve.yml index 252467e03..3f4c8aff1 100644 --- a/.github/workflows/ci_serve.yml +++ b/.github/workflows/ci_serve.yml @@ -17,7 +17,7 @@ jobs: os: [ubuntu-22.04] steps: - uses: actions/checkout@v4 - - uses: prefix-dev/setup-pixi@v0.8.10 + - uses: prefix-dev/setup-pixi@v0.9.4 with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} diff --git a/.github/workflows/ci_xtb.yml b/.github/workflows/ci_xtb.yml index c3d6c2b2d..712730bae 100644 --- a/.github/workflows/ci_xtb.yml +++ b/.github/workflows/ci_xtb.yml @@ -20,7 +20,7 @@ jobs: os: [ubuntu-22.04] steps: - uses: actions/checkout@v4 - - uses: prefix-dev/setup-pixi@v0.8.10 + - uses: prefix-dev/setup-pixi@v0.9.4 with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} diff --git a/pixi.lock b/pixi.lock index 207c713cf..496140c5d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -890,7 +890,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h171cf75_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/fmt-12.0.0-h2b0788b_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/fmt-11.2.0-h07f6e7f_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/fortran-compiler-1.10.0-h36df796_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/gcc-13.3.0-h9576a4e_2.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-13.3.0-h1e990d8_2.conda @@ -1005,7 +1005,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/scipy-1.16.3-py312h7a1785b_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/simple-dftd3-1.2.1-h3b12eaf_1.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/spdlog-1.16.0-hffee6e0_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/spdlog-1.16.0-ha91398d_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/stack_data-0.6.3-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.28-h4ee821c_8.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/tblite-0.4.0-hd37a5e2_2.conda @@ -1112,7 +1112,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/eigen-3.4.0-h49c215f_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.3-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/osx-arm64/fmt-12.1.0-h403dcb5_0.conda + - conda: https://conda.anaconda.org/conda-forge/osx-arm64/fmt-11.2.0-h440487c_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/fortran-compiler-1.10.0-h5692697_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/gfortran-13.2.0-h1ca8e4b_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/gfortran_impl_osx-arm64-13.2.0-h252ada1_3.conda @@ -1220,7 +1220,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/sigtool-0.1.3-h98dc951_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/sigtool-codesign-0.1.3-h98dc951_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/simple-dftd3-1.2.1-hb42fc24_1.conda - - conda: https://conda.anaconda.org/conda-forge/osx-arm64/spdlog-1.17.0-ha0f8610_1.conda + - conda: https://conda.anaconda.org/conda-forge/osx-arm64/spdlog-1.16.0-h06f2c6e_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/stack_data-0.6.3-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/tapi-1300.6.5-h03f4b80_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/tblite-0.4.0-hb3fdf34_2.conda @@ -1920,7 +1920,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h171cf75_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/fmt-12.0.0-h2b0788b_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/fmt-11.2.0-h07f6e7f_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/fortran-compiler-1.10.0-h36df796_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/gcc-13.3.0-h9576a4e_2.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-13.3.0-h1e990d8_2.conda @@ -2008,7 +2008,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/rust-std-x86_64-unknown-linux-gnu-1.93.1-h2c6d0dc_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/sccache-0.14.0-he64ecbb_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/spdlog-1.16.0-hffee6e0_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/spdlog-1.16.0-ha91398d_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/stack_data-0.6.3-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.28-h4ee821c_8.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/tinyxml2-11.0.0-h3f2d84a_0.conda @@ -2109,7 +2109,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/eigen-3.4.0-h49c215f_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.3-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/osx-arm64/fmt-12.1.0-h403dcb5_0.conda + - conda: https://conda.anaconda.org/conda-forge/osx-arm64/fmt-11.2.0-h440487c_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/fortran-compiler-1.10.0-h5692697_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/gfortran-13.2.0-h1ca8e4b_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/gfortran_impl_osx-arm64-13.2.0-h252ada1_3.conda @@ -2199,7 +2199,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-80.10.1-pyh332efcf_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/sigtool-0.1.3-h98dc951_0.conda - 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name: Install cbindgen + run: pixi run ensure_cbindgen + - name: Build run: | pixi run bash -c "meson setup bbdir \ diff --git a/.github/workflows/ci_build_akmc.yml b/.github/workflows/ci_build_akmc.yml index 500f35d86..1c041f164 100644 --- a/.github/workflows/ci_build_akmc.yml +++ b/.github/workflows/ci_build_akmc.yml @@ -27,6 +27,10 @@ jobs: script: | core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); + - name: Install cbindgen + shell: pixi run bash -e {0} + run: pixi run ensure_cbindgen + - name: Use Homebrew gfortran (macOS) if: runner.os == 'macOS' run: | diff --git a/.github/workflows/ci_build_gprd.yml b/.github/workflows/ci_build_gprd.yml index 2cc39da23..b502bce99 100644 --- a/.github/workflows/ci_build_gprd.yml +++ b/.github/workflows/ci_build_gprd.yml @@ -37,6 +37,10 @@ jobs: script: | core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); + - name: Install cbindgen + shell: pixi run bash -e {0} + run: pixi run ensure_cbindgen + - name: Install eon shell: pixi run bash -e {0} run: | diff --git a/.github/workflows/ci_metatomic.yml b/.github/workflows/ci_metatomic.yml index 42f463973..7d117713e 100644 --- a/.github/workflows/ci_metatomic.yml +++ b/.github/workflows/ci_metatomic.yml @@ -31,6 +31,10 @@ jobs: script: | core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); + - name: Install cbindgen + shell: pixi run bash -e {0} + run: pixi run ensure_cbindgen + - name: Use Homebrew gfortran (macOS) if: runner.os == 'macOS' run: | diff --git a/.github/workflows/ci_serve.yml b/.github/workflows/ci_serve.yml index 3f4c8aff1..16d66f1c7 100644 --- a/.github/workflows/ci_serve.yml +++ b/.github/workflows/ci_serve.yml @@ -30,6 +30,10 @@ jobs: script: | core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); + - name: Install cbindgen + shell: pixi run bash -e {0} + run: pixi run ensure_cbindgen + - name: Build with serve mode shell: pixi run bash -e {0} run: | diff --git a/.github/workflows/ci_xtb.yml b/.github/workflows/ci_xtb.yml index 712730bae..30469e9cd 100644 --- a/.github/workflows/ci_xtb.yml +++ b/.github/workflows/ci_xtb.yml @@ -33,6 +33,10 @@ jobs: script: | core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); + - name: Install cbindgen + shell: pixi run bash -e {0} + run: pixi run ensure_cbindgen + - name: Install eon shell: pixi run bash -e {0} run: | diff --git a/pixi.lock b/pixi.lock index 496140c5d..3290ccf07 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,6 +1,6 @@ version: 6 environments: - ams: + default: channels: - url: https://conda.anaconda.org/conda-forge/ indexes: @@ -10,309 +10,288 @@ environments: pypi-prerelease-mode: if-necessary-or-explicit packages: linux-64: - 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SPDLOG_LOGGER_DEBUG( - log, "[Basin Hopping] {:5d} {:12.3f} {:12.3f} {:12.3f} {:5.3f} {:5.3f} {:1s}", - step + 1, currentEnergy, minTrial->getPotentialEnergy(), - minimumEnergy, totalAccept / (static_cast(step) + 1), - curDisplacement, accepted ? "A" : "R"); + SPDLOG_LOGGER_DEBUG(log, + "[Basin Hopping] {:5d} {:12.3f} {:12.3f} {:12.3f} " + "{:5.3f} {:5.3f} {:1s}", + step + 1, currentEnergy, minTrial->getPotentialEnergy(), + minimumEnergy, + totalAccept / (static_cast(step) + 1), + curDisplacement, accepted ? "A" : "R"); bhFile.print("{:6d} {:12.4e} {:12.4e}\n", step + 1, currentEnergy, minTrial->getPotentialEnergy()); diff --git a/client/FiniteDifferenceJob.cpp b/client/FiniteDifferenceJob.cpp index 6625fb98d..69926d5fd 100644 --- a/client/FiniteDifferenceJob.cpp +++ b/client/FiniteDifferenceJob.cpp @@ -36,10 +36,10 @@ std::vector FiniteDifferenceJob::run(void) { AtomMatrix displacement; displacement.resize(reactant->numberOfAtoms(), 3); displacement.setZero(); - SPDLOG_DEBUG( "displacing atoms:"); + SPDLOG_DEBUG("displacing atoms:"); for (int i = 0; i < reactant->numberOfAtoms(); i++) { if (reactant->distance(epicenter, i) <= 3.3) { - SPDLOG_DEBUG( " {}", i); + SPDLOG_DEBUG(" {}", i); for (int j = 0; j < 3; j++) { if (!reactant->getFixed(i)) { displacement(i, j) = randomDouble(1.0); @@ -52,7 +52,7 @@ std::vector FiniteDifferenceJob::run(void) { // Loop over values of dimer dR and print the output to results.dat. auto results = fmt::output_file("results.dat"); results.print("{:>14s} {:>14s}\n", "dR", "curvature"); - SPDLOG_DEBUG( "{:>14s} {:>14s}", "dR", "curvature"); + SPDLOG_DEBUG("{:>14s} {:>14s}", "dR", "curvature"); AtomMatrix posB; AtomMatrix forceB; double curvature = 0.0; @@ -63,7 +63,7 @@ std::vector FiniteDifferenceJob::run(void) { curvature = ((forceB - forceA).array() * displacement.array()).sum() / dRs[dRi]; results.print("{:14.8f} {:14.8f}\n", dRs[dRi], curvature); - SPDLOG_DEBUG( "{:14.8f} {:14.8f}", dRs[dRi], curvature); + SPDLOG_DEBUG("{:14.8f} {:14.8f}", dRs[dRi], curvature); } std::vector empty; diff --git a/client/GlobalOptimizationJob.cpp b/client/GlobalOptimizationJob.cpp index 352d6969e..534f02687 100644 --- a/client/GlobalOptimizationJob.cpp +++ b/client/GlobalOptimizationJob.cpp @@ -191,8 +191,10 @@ void GlobalOptimizationJob::report(Matter *matter_hop) { double epot_hop = matter_hop->getPotentialEnergy(); double temp = (2.0 * ekin_p / params.constants.kB); double dt = params.dynamics_options.time_step; - monfile.print("{:15.5f} {:15.5f} {:11d} {:12.2f} {:c}{:c} {:5d} {:5d}", - epot_hop, ediff, static_cast(temp), dt, C1, C2, fcallsMove, fcallsRelax); + monfile.print( + "{:15.5f} {:15.5f} {:11d} {:12.2f} {:c}{:c} {:5d} {:5d}", + epot_hop, ediff, static_cast(temp), dt, C1, C2, fcallsMove, + fcallsRelax); } void GlobalOptimizationJob::decisionStep(Matter *matter_cur, diff --git a/client/Matter.h b/client/Matter.h index b347aedce..7c7903dfe 100644 --- a/client/Matter.h +++ b/client/Matter.h @@ -17,8 +17,8 @@ #include #include #include -#include #include +#include // This is a forward declaration of BondBoost to avoid a circular dependency. class BondBoost; @@ -167,12 +167,10 @@ class Matter { bool con2matter(std::string filename); // read con file into Matter, return // true if successful bool con2matter(const readcon::ConFrame &frame); // populate from a parsed - // readcon frame - bool - convel2matter(std::string filename); // read convel file via readcon-core - bool - matter2con(std::string filename, - bool append = false); // write con file via readcon-core + // readcon frame + bool convel2matter(std::string filename); // read convel file via readcon-core + bool matter2con(std::string filename, + bool append = false); // write con file via readcon-core bool matter2convel(std::string filename); // write convel file via readcon-core void matter2xyz(std::string filename, diff --git a/client/NudgedElasticBandJob.cpp b/client/NudgedElasticBandJob.cpp index 1d21cd640..3e1c0bce7 100644 --- a/client/NudgedElasticBandJob.cpp +++ b/client/NudgedElasticBandJob.cpp @@ -140,9 +140,8 @@ void NudgedElasticBandJob::saveData(NudgedElasticBand::NEBStatus status, { auto out = fmt::output_file(resultsFilename); out.print("{} termination_reason\n", static_cast(status)); - out.print("{} potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)}); + out.print("{} potential_type\n", std::string{magic_enum::enum_name( + params.potential_options.potential)}); out.print("{:f} energy_reference\n", neb->path[0]->getPotentialEnergy()); out.print("{} number_of_images\n", neb->numImages); @@ -153,10 +152,9 @@ void NudgedElasticBandJob::saveData(NudgedElasticBand::NEBStatus status, i); out.print("{:f} image{}_force\n", neb->path[i]->getForces().norm(), i); - double proj_norm = - (i >= 1 && i <= neb->numImages) - ? neb->projectedForce[i]->norm() - : 0.0; + double proj_norm = (i >= 1 && i <= neb->numImages) + ? neb->projectedForce[i]->norm() + : 0.0; out.print("{:f} image{}_projected_force\n", proj_norm, i); } diff --git a/client/ParallelReplicaJob.cpp b/client/ParallelReplicaJob.cpp index d81f681dd..ffc14e3c5 100644 --- a/client/ParallelReplicaJob.cpp +++ b/client/ParallelReplicaJob.cpp @@ -203,9 +203,8 @@ std::vector ParallelReplicaJob::run(void) { returnFiles.push_back(resultsFilename); { auto out = fmt::output_file(resultsFilename); - out.print("{} potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)}); + out.print("{} potential_type\n", std::string{magic_enum::enum_name( + params.potential_options.potential)}); out.print("{} random_seed\n", params.main_options.randomSeed); out.print("{:f} potential_energy_reactant\n", reactant->getPotentialEnergy()); diff --git a/client/ProcessSearchJob.cpp b/client/ProcessSearchJob.cpp index a5d034aa5..97dc6c829 100644 --- a/client/ProcessSearchJob.cpp +++ b/client/ProcessSearchJob.cpp @@ -241,9 +241,8 @@ void ProcessSearchJob::saveData(int status) { auto out = fmt::output_file(resultsFilename); out.print("{} termination_reason\n", status); out.print("{} random_seed\n", params.main_options.randomSeed); - out.print("{} potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)}); + out.print("{} potential_type\n", std::string{magic_enum::enum_name( + params.potential_options.potential)}); out.print("{} total_force_calls\n", fCallsMin + fCallsSaddle + fCallsPrefactors); out.print("{} force_calls_minimization\n", fCallsMin); @@ -252,8 +251,7 @@ void ProcessSearchJob::saveData(int status) { saddle->getPotentialEnergy()); out.print("{:.12e} potential_energy_reactant\n", min1->getPotentialEnergy()); - out.print("{:.12e} potential_energy_product\n", - min2->getPotentialEnergy()); + out.print("{:.12e} potential_energy_product\n", min2->getPotentialEnergy()); out.print("{:.12e} barrier_reactant_to_product\n", barriersValues[0]); out.print("{:.12e} barrier_product_to_reactant\n", barriersValues[1]); if (params.saddle_search_options.method == "min_mode") { @@ -280,7 +278,8 @@ void ProcessSearchJob::saveData(int status) { std::string modeFilename("mode.dat"); returnFiles.push_back(modeFilename); - helper_functions::saveMode(modeFilename, saddle, saddleSearch->getEigenvector()); + helper_functions::saveMode(modeFilename, saddle, + saddleSearch->getEigenvector()); std::string saddleFilename("saddle.con"); returnFiles.push_back(saddleFilename); diff --git a/client/ReplicaExchangeJob.cpp b/client/ReplicaExchangeJob.cpp index adb762325..fec45d4d4 100644 --- a/client/ReplicaExchangeJob.cpp +++ b/client/ReplicaExchangeJob.cpp @@ -137,9 +137,8 @@ void ReplicaExchangeJob::saveData(void) { { auto out = fmt::output_file(resultsFilename); out.print("{} random_seed\n", params.main_options.randomSeed); - out.print("{} potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)}); + out.print("{} potential_type\n", std::string{magic_enum::enum_name( + params.potential_options.potential)}); } std::string posFilename("pos_out.con"); diff --git a/client/SaddleSearchJob.cpp b/client/SaddleSearchJob.cpp index e2442a6b7..685cbe65d 100644 --- a/client/SaddleSearchJob.cpp +++ b/client/SaddleSearchJob.cpp @@ -101,15 +101,13 @@ void SaddleSearchJob::saveData(int status) { out.print("{} termination_reason\n", status); out.print("saddle_search job_type\n"); out.print("{} random_seed\n", params.main_options.randomSeed); - out.print("{} potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)}); + out.print("{} potential_type\n", std::string{magic_enum::enum_name( + params.potential_options.potential)}); out.print("{} total_force_calls\n", this->pot->forceCallCounter); out.print("{} force_calls_saddle\n", fCallsSaddle); out.print("{} iterations\n", saddleSearch->iteration); if (status != MinModeSaddleSearch::STATUS_POTENTIAL_FAILED) { - out.print("{:f} potential_energy_saddle\n", - saddle->getPotentialEnergy()); + out.print("{:f} potential_energy_saddle\n", saddle->getPotentialEnergy()); out.print("{:f} final_eigenvalue\n", saddleSearch->getEigenvalue()); } out.print("{:f} potential_energy_reactant\n", @@ -118,7 +116,8 @@ void SaddleSearchJob::saveData(int status) { std::string modeFilename("mode.dat"); returnFiles.push_back(modeFilename); - helper_functions::saveMode(modeFilename, saddle, saddleSearch->getEigenvector()); + helper_functions::saveMode(modeFilename, saddle, + saddleSearch->getEigenvector()); std::string saddleFilename("saddle.con"); returnFiles.push_back(saddleFilename); diff --git a/client/SafeHyperJob.cpp b/client/SafeHyperJob.cpp index 026a16902..e40ce64c8 100644 --- a/client/SafeHyperJob.cpp +++ b/client/SafeHyperJob.cpp @@ -291,9 +291,8 @@ void SafeHyperJob::saveData(int status) { { auto out = fmt::output_file(resultsFilename); - out.print("{} potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)}); + out.print("{} potential_type\n", std::string{magic_enum::enum_name( + params.potential_options.potential)}); out.print("{} random_seed\n", params.main_options.randomSeed); out.print("{:f} potential_energy_reactant\n", reactant->getPotentialEnergy()); @@ -312,9 +311,8 @@ void SafeHyperJob::saveData(int status) { out.print("{:e} simulation_time_s\n", time * 1.0e-15 * params.constants.timeUnit); - out.print("{:f} speedup\n", - time / params.dynamics_options.steps / - params.dynamics_options.time_step); + out.print("{:f} speedup\n", time / params.dynamics_options.steps / + params.dynamics_options.time_step); } std::string reactantFilename("reactant.con"); diff --git a/client/TADJob.cpp b/client/TADJob.cpp index bf901a542..aec880243 100644 --- a/client/TADJob.cpp +++ b/client/TADJob.cpp @@ -281,9 +281,8 @@ void TADJob::saveData(int status) { { auto out = fmt::output_file(resultsFilename); - out.print("{} potential_type\n", - std::string{magic_enum::enum_name( - params.potential_options.potential)}); + out.print("{} potential_type\n", std::string{magic_enum::enum_name( + params.potential_options.potential)}); out.print("{} random_seed\n", params.main_options.randomSeed); out.print("{:f} potential_energy_reactant\n", reactant->getPotentialEnergy()); @@ -302,9 +301,8 @@ void TADJob::saveData(int status) { out.print("{:e} simulation_time_s\n", time * 1.0e-15 * params.constants.timeUnit); - out.print("{:f} speedup\n", - time / params.dynamics_options.steps / - params.dynamics_options.time_step); + out.print("{:f} speedup\n", time / params.dynamics_options.steps / + params.dynamics_options.time_step); } std::string reactantFilename("reactant.con"); From 5079fe87e3fd2b23e9a14645d85e08104f1487d0 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 12:53:26 +0100 Subject: [PATCH 08/22] feat(py): replace fileio con I/O with readcon package loadcon/loadcons/savecon now delegate to readcon.read_con, readcon.read_con_string, readcon.write_con, and readcon.write_con_string. Preserves StringIO support for server communication and append mode for multi-frame files. --- eon/fileio.py | 147 ++++++++++++++++++++------------------------------ 1 file changed, 58 insertions(+), 89 deletions(-) diff --git a/eon/fileio.py b/eon/fileio.py index 333d718df..4230048c8 100644 --- a/eon/fileio.py +++ b/eon/fileio.py @@ -11,6 +11,7 @@ import os import pickle as pickle +import readcon from eon import atoms from eon.config import config @@ -52,14 +53,24 @@ def box_to_length_angle(box): return lengths, angles +def _frame_to_atoms(frame): + '''Convert a readcon.ConFrame to an eon Atoms object.''' + num_atoms = len(frame) + a = atoms.Atoms(num_atoms) + boxlengths = numpy.array(list(frame.cell)) + boxangles = numpy.array(list(frame.angles)) + a.box = length_angle_to_box(boxlengths, boxangles) + for i, atom in enumerate(frame.atoms): + a.r[i] = [atom.x, atom.y, atom.z] + a.names[i] = atom.symbol + a.mass[i] = atom.mass if atom.mass is not None else 0.0 + a.free[i] = 0 if atom.is_fixed else 1 + return a + + def loadcons(filename): - filein = open(filename, 'r') - p = [] - while True: - try: - p.append(loadcon(filein, reset=False)) - except: - return p + frames = readcon.read_con(filename) + return [_frame_to_atoms(f) for f in frames] def loadposcars(filename): @@ -78,57 +89,38 @@ def loadcon(filein, reset = True): filein: may be either a filename or a file-like object ''' if hasattr(filein, 'readline'): - con = filein + # File-like object (e.g. StringIO from server communication) + content = filein.read() + if reset: + filein.seek(0) + frames = readcon.read_con_string(content) else: - con = open(filein, 'r') - con.readline() # line 1: comment - con.readline() # line 2: comment - # determine how many dimensions - tmp = numpy.array(con.readline().split()) # line 3: Box lengths - for i in range(len(tmp)): - dim=i+1 - try: float(tmp[i]) - except: - dim=i - break - # handle the box - boxlengths=numpy.zeros(dim) - for i in range(dim): - boxlengths[i]=float(tmp[i]) - boxangles=numpy.array([ float(f) for f in con.readline().split()[0:dim] ]) # line 4: Box angles - boxtemp=numpy.zeros((dim,dim),'d') - boxtemp = length_angle_to_box(boxlengths,boxangles) - con.readline() # line 5: comment - con.readline() # line 6: comment - num_types = int(con.readline().split()[0]) # line 7: number of atom types - num_each_type = con.readline().split() # line 8: number of each type of atom - mass_of_type = con.readline().split() # line 9: mass of each type of atom - num_atoms = 0 - for i in range(num_types): - num_each_type[i] = int(num_each_type[i]) - mass_of_type[i] = float(mass_of_type[i]) - num_atoms += num_each_type[i] - a = atoms.Atoms(num_atoms) - a.box = boxtemp - index = 0 - for i in range(num_types): - name = con.readline().strip() - if abs(1.0-mass_of_type[i]) < 1e-6 and name != "H": - logger.warning("WARNING: Mass of %s set to 1.0", name) - - con.readline() # skip meaningless line - for j in range(num_each_type[i]): - vals = con.readline().split() - for k in range(dim): - a.r[index][k] = float(vals[k]) - a.mass[index] = mass_of_type[i] - a.names[index] = name - if not int(vals[dim])==0: - a.free[index]=0 - index += 1 - if reset: - con.seek(0) - return a + frames = readcon.read_con(filein) + if not frames: + raise IOError("No frames found in con data") + return _frame_to_atoms(frames[0]) + +def _atoms_to_frame(p): + '''Convert an eon Atoms object to a readcon.ConFrame.''' + lengths, angles = box_to_length_angle(p.box) + atom_list = [] + for i in range(len(p)): + atom_list.append(readcon.Atom( + symbol=p.names[i], + x=float(p.r[i][0]), + y=float(p.r[i][1]), + z=float(p.r[i][2]), + is_fixed=(p.free[i] == 0), + atom_id=i + 1, + mass=float(p.mass[i]), + )) + return readcon.ConFrame( + cell=list(lengths), + angles=list(angles), + atoms=atom_list, + prebox_header=["Generated by eOn", ""], + ) + def savecon(fileout, p, w = 'w'): ''' @@ -137,41 +129,18 @@ def savecon(fileout, p, w = 'w'): p: information (in the form of an atoms object) to save w: write/append flag ''' + frame = _atoms_to_frame(p) if hasattr(fileout, 'write'): - con = fileout + # File-like object (e.g. StringIO for server communication) + text = readcon.write_con_string([frame]) + fileout.write(text) else: - con = open(fileout, w) - con.write("Generated by eOn\n\n") - dim = len(p.r[0]) - lengths, angles = box_to_length_angle(p.box) - con.write(" ".join(['%.6f' % s for s in lengths])+"\n") - con.write(" ".join(['%.6f' % s for s in angles])+"\n") - con.write("\n\n") - atom_count = {} - name_order = [] - for i in range(len(p)): - name = p.names[i] - if name not in name_order: - name_order.append(name) - if name in atom_count: - atom_count[name] += 1 + if w == 'a' and os.path.exists(fileout): + existing = readcon.read_con(fileout) + existing.append(frame) + readcon.write_con(fileout, existing) else: - atom_count[name] = 1 - con.write(str(len(name_order))+"\n") - con.write(" ".join([str(atom_count[i]) for i in name_order])+"\n") - printmasses = [] - index = 0 - for i in range(len(name_order)): - printmasses.append(p.mass[index]) - index += atom_count[name_order[i]] - con.write(" ".join(["%.6f"% i for i in printmasses])+"\n") - index = 0 - for i in range(len(name_order)): - con.write(name_order[i]+"\n") - con.write("Coordinates of component %3i" %(i+1)+"\n") - for j in range(atom_count[name_order[i]]): - con.write("%.6f %.6f %.6f %d %d\n" %( p.r[index][0], p.r[index][1], p.r[index][2], int(not p.free[index]), index+1)) - index += 1 + readcon.write_con(fileout, [frame]) def load_mode(modefilein): From 07a203299877a26be89fb4cb824fa049d7bdf8c0 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 12:53:32 +0100 Subject: [PATCH 09/22] bld: replace PDM with uv for dependency management Remove tool.pdm sections, move dev-dependencies to dependency-groups. 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Use direct cargo install in benchmark CI (main lacks the task). Switch docs CI from pdm to uv sync --group docs. --- .github/workflows/ci_benchmark.yml | 3 ++- .github/workflows/ci_docs.yml | 6 +++--- pixi.toml | 2 +- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci_benchmark.yml b/.github/workflows/ci_benchmark.yml index 94d886ae2..598e1e45a 100644 --- a/.github/workflows/ci_benchmark.yml +++ b/.github/workflows/ci_benchmark.yml @@ -51,7 +51,8 @@ jobs: core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); - name: Install cbindgen - run: pixi run ensure_cbindgen + shell: bash + run: command -v cbindgen || cargo install cbindgen - name: Build run: | diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml index c87827411..dc8d7d06b 100644 --- a/.github/workflows/ci_docs.yml +++ b/.github/workflows/ci_docs.yml @@ -39,9 +39,9 @@ jobs: - name: Generate Docs shell: pixi run bash -e {0} run: | - uvx pdm sync - uvx pdm run pip install . -vvv - uvx pdm run sphinx-build -b html docs/source docs/build/html + uv sync --group docs --no-install-project + uv pip install . -vvv --no-build-isolation + uv run sphinx-build -b html docs/source docs/build/html - name: Upload artifact uses: actions/upload-artifact@v4 diff --git a/pixi.toml b/pixi.toml index 3dd993831..0451b1008 100644 --- a/pixi.toml +++ b/pixi.toml @@ -9,7 +9,7 @@ version = "2.11.0" [tasks] # cbindgen is not on conda-forge; install via cargo if missing -ensure_cbindgen = "command -v cbindgen >/dev/null 2>&1 || cargo install cbindgen" +ensure_cbindgen = "command -v cbindgen > /dev/null || cargo install cbindgen" [dependencies] eigen = ">=3.4,<3.5" From ae66dd5e459a605f8b05b03fed37271f11916c7e Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 12:53:51 +0100 Subject: [PATCH 11/22] docs: update confile design docs and install guide Reflect that both read and write now use readcon-core. Add Python server section. Fix pixi reference in install guide. --- docs/source/devdocs/design/client/confile.md | 50 +++++++++++++++----- docs/source/install/index.md | 2 +- 2 files changed, 38 insertions(+), 14 deletions(-) diff --git a/docs/source/devdocs/design/client/confile.md b/docs/source/devdocs/design/client/confile.md index b76735fd1..5c9f376a9 100644 --- a/docs/source/devdocs/design/client/confile.md +++ b/docs/source/devdocs/design/client/confile.md @@ -8,22 +8,39 @@ myst: # .con file I/O eOn uses [readcon-core](https://github.com/lode-org/readcon-core), a Rust -library with C/C++ FFI, for reading `.con` files. The library is included as a -Meson subproject via `subprojects/readcon-core.wrap`. +library with C/C++ FFI and Python bindings, for all `.con` file reading and +writing. The library is included as a Meson subproject via +`subprojects/readcon-core.wrap` for the C++ client, and as a PyPI dependency +(`readcon`) for the Python server. -## Reading (`con2matter`) +## C++ client -`Matter::con2matter(std::string)` opens the file through -`readcon::ConFrameIterator` and extracts the first frame. -`Matter::con2matter(const readcon::ConFrame &)` then populates positions, cell, -masses, atomic numbers and fixed-atom flags from the frame's cached data. +### Reading (`con2matter`) -## Writing (`matter2con`) +`Matter::con2matter(std::string)` calls `readcon::read_first_frame()` (mmap +based) and passes the result to `Matter::con2matter(const readcon::ConFrame &)` +which populates positions, cell, masses, atomic numbers and fixed-atom flags. -Writing is still handled by `Matter::matter2con` using `FILE *` I/O, because -readcon-core's writer can only serialise opaque `RKRConFrame` handles that -originated from a previous read. Once readcon-core gains a frame-builder API, -the write path can be migrated as well. +### Writing (`matter2con`) + +`Matter::matter2con(std::string)` builds a `readcon::ConFrameBuilder` from the +current Matter state, calls `build()`, and writes the resulting frame via +`readcon::ConFrameWriter` with precision 17 (matching the previous `%22.17f` +format for lossless floating-point roundtrip). + +### Velocity files (`convel2matter` / `matter2convel`) + +The same readcon-core reader and builder handle `.convel` files, which extend +`.con` with a velocity section per atom type. + +## Python server + +`eon/fileio.py` uses the `readcon` Python package: + +- `loadcon()` / `loadcons()` call `readcon.read_con()` or + `readcon.read_con_string()` and convert frames to eOn `Atoms` objects. +- `savecon()` converts `Atoms` to `readcon.ConFrame` and writes with + `readcon.write_con()` or `readcon.write_con_string()` (for StringIO). ## Build requirements @@ -33,5 +50,12 @@ via `cargo install cbindgen` if not already present (see the `ensure_cbindgen` pixi task). ```{versionadded} 2.11 -Replaced the hand-written C `sscanf`/`fgets` parser with readcon-core. +Replaced the hand-written C `sscanf`/`fgets` parser with readcon-core for +reading. +``` + +```{versionchanged} 2.12 +Replaced `FILE *`/`fprintf` writing with readcon-core `ConFrameBuilder` + +`ConFrameWriter` for both C++ and Python. The Python server now uses the +`readcon` PyPI package instead of custom parsing in `fileio.py`. ``` diff --git a/docs/source/install/index.md b/docs/source/install/index.md index 9dc20375b..868633396 100644 --- a/docs/source/install/index.md +++ b/docs/source/install/index.md @@ -57,7 +57,7 @@ cd eOn ## Building from source -We provide a `conda` environment and `pixi` setup, with dependencies handled by `conda-lock`. +We provide a `conda` environment and `pixi` setup, with dependencies handled by `pixi`. ```{code-block} bash pixi shell From 47d39921fcdb8f1b2e092714e80090ce657b95cb Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 19:28:31 +0100 Subject: [PATCH 12/22] perf(deps): update readcon-core to v0.4.3 v0.4.3 uses read_to_string for files under 64 KiB instead of mmap, avoiding fixed VMA/page-fault overhead for small .con files. Also adds a dedicated read_first_frame path that stops after one frame. --- pyproject.toml | 2 +- subprojects/readcon-core.wrap | 2 +- uv.lock | 58 +++++++++++++++++------------------ 3 files changed, 31 insertions(+), 31 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7e5f48d67..b151eeee7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ authors = [ ] dependencies = [ "numpy>=1.26.4", - "readcon>=0.4.2", + "readcon>=0.4.3", ] requires-python = ">=3.11" # readme = "readme.md" diff --git a/subprojects/readcon-core.wrap b/subprojects/readcon-core.wrap index 23b26ac91..e34919997 100644 --- a/subprojects/readcon-core.wrap +++ b/subprojects/readcon-core.wrap @@ -1,7 +1,7 @@ [wrap-git] directory = readcon-core url = https://github.com/lode-org/readcon-core.git -revision = v0.4.2 +revision = v0.4.3 depth = 1 [provide] diff --git a/uv.lock b/uv.lock index 693df46d0..a27af9d51 100644 --- a/uv.lock +++ b/uv.lock @@ -457,7 +457,7 @@ testing = [ [package.metadata] 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update docbuild for uv, document extra-index pitfall The pixi workspace sets UV_EXTRA_INDEX_URL to the PyTorch CPU wheel index. Running uv lock inside a pixi shell picks this up and resolves packages against the PyTorch index, which can produce lockfiles with incompatible wheels for CI. Documented the workaround (unset the variable before running uv lock) and updated all PDM references to uv throughout. --- docs/source/devdocs/docbuild.md | 47 ++++++++++++++++++++++++--------- 1 file changed, 34 insertions(+), 13 deletions(-) diff --git a/docs/source/devdocs/docbuild.md b/docs/source/devdocs/docbuild.md index 3017e41f7..09c7bf0a9 100644 --- a/docs/source/devdocs/docbuild.md +++ b/docs/source/devdocs/docbuild.md @@ -1,8 +1,8 @@ --- myst: html_meta: - "description": "Instructions for building and working with the eOn documentation, including setup with PDM, local building, and adding citations and extensions." - "keywords": "eOn docs, build documentation, Sphinx, MyST, PDM, autodoc-pydantic" + "description": "Instructions for building and working with the eOn documentation, including setup with uv, local building, and adding citations and extensions." + "keywords": "eOn docs, build documentation, Sphinx, MyST, uv, autodoc-pydantic" --- # Working with the documentation @@ -16,28 +16,27 @@ The input file format transitioned to TOML from previously being an enhanced INI ## Setup -Although we use `micromamba` for handling system dependencies, the documenation +Although we use `pixi` for handling system dependencies, the documentation is handled via the `python` ecosystem. Namely: -- [PDM](https://pdm-project.org/en/latest/) is used to track versions, and provide [development groups](https://pdm-project.org/latest/usage/dependency/#add-development-only-dependencies) - -To facilitate interactions with `pdm`, -[uvx](https://docs.astral.sh/uv/getting-started/installation//) is recommended. +- [uv](https://docs.astral.sh/uv/) is used to manage the lockfile and dependency groups defined in `pyproject.toml` ## Building locally ````{margin} ```{note} -`uvx` simplifies running Python commands, and `pdm` handles version updates better, syncing nicely with the `pyproject.toml` so no Python dependencies not needed by the client should be in the `environment.yml` +`uv` manages dependency groups declared in `pyproject.toml` under +`[dependency-groups]`. System-level dependencies (compilers, etc.) +are handled separately by `pixi`. ``` ```` ```{code-block} bash # Setup dependencies -uvx pdm sync +uv sync --group docs --no-install-project # Need to install for autodoc-pydantic -uvx pdm run pip install . -vvv -uvx pdm run sphinx-build -b html docs/source docs/build/html +uv pip install . -vvv --no-build-isolation +uv run sphinx-build -b html docs/source docs/build/html ``` This can be viewed locally with an HTTP server. @@ -46,6 +45,28 @@ This can be viewed locally with an HTTP server. python -m http.server docs/build/html ``` +### Extra-index pitfall + +The `pixi.toml` workspace sets `extra-index-urls` pointing at the PyTorch CPU +wheel index and uses `index-strategy = "unsafe-best-match"`. When pixi +activates an environment, these propagate as `UV_EXTRA_INDEX_URL` and +`PIP_EXTRA_INDEX_URL` environment variables. + +If you regenerate `uv.lock` from inside a pixi shell, `uv lock` will resolve +packages against the PyTorch index as well as PyPI. The PyTorch index carries +only a subset of wheels (often only the latest CPython pre-release), so +packages like `markupsafe` can resolve to versions with no compatible wheel for +the CI Python version. + +To avoid this, always regenerate the lockfile with the extra-index variables +unset: + +```{code-block} bash +UV_EXTRA_INDEX_URL="" PIP_EXTRA_INDEX_URL="" uv lock --upgrade +``` + +Alternatively, run `uv lock` outside of any pixi environment. + ## Writing documentation We use `myst` markdown via the `myst-parser` extension for almost everything, @@ -61,10 +82,10 @@ The following sections detail methods to add functionality to the documentation. ## Adding extensions -Additions to the build process are handled by the `pdm` development group `docs`, so additions are done via: +Additions to the build process are handled by the `docs` dependency group, so additions are done via: ```{code-block} bash -uvx pdm add -dG docs "sphinxcontrib-bibtex" +uv add --group docs "sphinxcontrib-bibtex" ``` ## Adding citations From 783bb12614c6ea41eb2cc9884c91c12924f2a645 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 19:50:39 +0100 Subject: [PATCH 15/22] fix(ci): install build deps before no-isolation pip install, update devdocs The docs workflow uses --no-build-isolation so uv skips installing build-system.requires (meson-python, numpy). Install them explicitly. Also updated docbuild.md from PDM to uv and documented the UV_EXTRA_INDEX_URL pitfall when regenerating uv.lock inside a pixi environment that sets extra-index-urls for the PyTorch wheel index. --- .github/workflows/ci_docs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml index dc8d7d06b..d3ae241e5 100644 --- a/.github/workflows/ci_docs.yml +++ b/.github/workflows/ci_docs.yml @@ -40,6 +40,7 @@ jobs: shell: pixi run bash -e {0} run: | uv sync --group docs --no-install-project + uv pip install meson-python numpy uv pip install . -vvv --no-build-isolation uv run sphinx-build -b html docs/source docs/build/html From a08ccc7f3dfb230dd4c0e415a518ae2e5b3baa36 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 19:56:15 +0100 Subject: [PATCH 16/22] fix(ci): use PYTHONPATH instead of pip install for docs build The eon Python package is pure Python and does not need C++ extension compilation for documentation. Using pip install triggers mesonpy which requires cbindgen, cargo, and the full toolchain. Setting PYTHONPATH to the repo root makes the package importable for autodoc-pydantic without building anything. --- .github/workflows/ci_docs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml index d3ae241e5..8829ba88a 100644 --- a/.github/workflows/ci_docs.yml +++ b/.github/workflows/ci_docs.yml @@ -38,10 +38,10 @@ jobs: - name: Generate Docs shell: pixi run bash -e {0} + env: + PYTHONPATH: ${{ github.workspace }} run: | uv sync --group docs --no-install-project - uv pip install meson-python numpy - uv pip install . -vvv --no-build-isolation uv run sphinx-build -b html docs/source docs/build/html - name: Upload artifact From d046fcd9174bd9fcb97918e3f612030d26924bf8 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 19:57:12 +0100 Subject: [PATCH 17/22] fix(deps): use commit hash in readcon-core.wrap for shallow clone Annotated tags do not dereference properly with depth=1 shallow clones in meson wraps, producing "is not a commit" warnings. Use the commit hash for v0.4.3 directly. --- subprojects/readcon-core.wrap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subprojects/readcon-core.wrap b/subprojects/readcon-core.wrap index e34919997..b8fd9036b 100644 --- a/subprojects/readcon-core.wrap +++ b/subprojects/readcon-core.wrap @@ -1,7 +1,7 @@ [wrap-git] directory = readcon-core url = https://github.com/lode-org/readcon-core.git -revision = v0.4.3 +revision = d797dc3c185b2d0ceb7bf37b06c6d63749c9fdb1 depth = 1 [provide] From 31f193a3ff71a38f291fad4e6ed276f2b421d591 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 20:02:42 +0100 Subject: [PATCH 18/22] fix(ci): pass --no-project to uv run in docs build uv run implicitly builds and installs the project, triggering the full mesonpy build (C++, Rust subprojects, cbindgen). The docs only need the pure-Python eon package, which is already on PYTHONPATH. Adding --no-project prevents uv from attempting to build. --- .github/workflows/ci_docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml index 8829ba88a..94825d307 100644 --- a/.github/workflows/ci_docs.yml +++ b/.github/workflows/ci_docs.yml @@ -42,7 +42,7 @@ jobs: PYTHONPATH: ${{ github.workspace }} run: | uv sync --group docs --no-install-project - uv run sphinx-build -b html docs/source docs/build/html + uv run --no-project sphinx-build -b html docs/source docs/build/html - name: Upload artifact uses: actions/upload-artifact@v4 From 16bcc48712e73e45df751cfbc61d1410fc596e2a Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 20:05:03 +0100 Subject: [PATCH 19/22] fix(ci): use shell: bash for cbindgen install across all workflows pixi run bash on Windows triggers vcvarsall.bat activation which hits the CMD line length limit. Use plain bash shell with direct cargo install instead of pixi run ensure_cbindgen in all CI workflows. --- .github/workflows/ci_build_akmc.yml | 4 ++-- .github/workflows/ci_build_gprd.yml | 4 ++-- .github/workflows/ci_metatomic.yml | 4 ++-- .github/workflows/ci_serve.yml | 4 ++-- .github/workflows/ci_xtb.yml | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci_build_akmc.yml b/.github/workflows/ci_build_akmc.yml index 1c041f164..3eff0160b 100644 --- a/.github/workflows/ci_build_akmc.yml +++ b/.github/workflows/ci_build_akmc.yml @@ -28,8 +28,8 @@ jobs: core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); - name: Install cbindgen - shell: pixi run bash -e {0} - run: pixi run ensure_cbindgen + shell: bash + run: command -v cbindgen || cargo install cbindgen - name: Use Homebrew gfortran (macOS) if: runner.os == 'macOS' diff --git a/.github/workflows/ci_build_gprd.yml b/.github/workflows/ci_build_gprd.yml index b502bce99..da4c852c8 100644 --- a/.github/workflows/ci_build_gprd.yml +++ b/.github/workflows/ci_build_gprd.yml @@ -38,8 +38,8 @@ jobs: core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); - name: Install cbindgen - shell: pixi run bash -e {0} - run: pixi run ensure_cbindgen + shell: bash + run: command -v cbindgen || cargo install cbindgen - name: Install eon shell: pixi run bash -e {0} diff --git a/.github/workflows/ci_metatomic.yml b/.github/workflows/ci_metatomic.yml index 7d117713e..0c69fb4fc 100644 --- a/.github/workflows/ci_metatomic.yml +++ b/.github/workflows/ci_metatomic.yml @@ -32,8 +32,8 @@ jobs: core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); - name: Install cbindgen - shell: pixi run bash -e {0} - run: pixi run ensure_cbindgen + shell: bash + run: command -v cbindgen || cargo install cbindgen - name: Use Homebrew gfortran (macOS) if: runner.os == 'macOS' diff --git a/.github/workflows/ci_serve.yml b/.github/workflows/ci_serve.yml index 16d66f1c7..6bfbee4dd 100644 --- a/.github/workflows/ci_serve.yml +++ b/.github/workflows/ci_serve.yml @@ -31,8 +31,8 @@ jobs: core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); - name: Install cbindgen - shell: pixi run bash -e {0} - run: pixi run ensure_cbindgen + shell: bash + run: command -v cbindgen || cargo install cbindgen - name: Build with serve mode shell: pixi run bash -e {0} diff --git a/.github/workflows/ci_xtb.yml b/.github/workflows/ci_xtb.yml index 30469e9cd..876cdbda1 100644 --- a/.github/workflows/ci_xtb.yml +++ b/.github/workflows/ci_xtb.yml @@ -34,8 +34,8 @@ jobs: core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || ''); core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || ''); - name: Install cbindgen - shell: pixi run bash -e {0} - run: pixi run ensure_cbindgen + shell: bash + run: command -v cbindgen || cargo install cbindgen - name: Install eon shell: pixi run bash -e {0} From f3b4beb49c3222ba29cca072540c80c8e5f68e8a Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 20:10:17 +0100 Subject: [PATCH 20/22] docs: add towncrier fragments for readcon migration and uv switch Fragments cover: - C++ client con I/O replaced with readcon-core FFI - Python fileio replaced with readcon package - readcon-core added as meson subproject dependency - FILE*/fprintf replaced with fmt::output_file in Job files - PDM replaced with uv for Python dependency management --- docs/newsfragments/+fmtfile.client.changed.md | 1 + docs/newsfragments/+readcon.client.added.md | 1 + docs/newsfragments/+readcon.client.changed.md | 1 + docs/newsfragments/+readcon.fileio.changed.md | 1 + docs/newsfragments/+uv.dev.changed.md | 1 + 5 files changed, 5 insertions(+) create mode 100644 docs/newsfragments/+fmtfile.client.changed.md create mode 100644 docs/newsfragments/+readcon.client.added.md create mode 100644 docs/newsfragments/+readcon.client.changed.md create mode 100644 docs/newsfragments/+readcon.fileio.changed.md create mode 100644 docs/newsfragments/+uv.dev.changed.md diff --git a/docs/newsfragments/+fmtfile.client.changed.md b/docs/newsfragments/+fmtfile.client.changed.md new file mode 100644 index 000000000..07119d57c --- /dev/null +++ b/docs/newsfragments/+fmtfile.client.changed.md @@ -0,0 +1 @@ +Replace ``FILE*``/``fprintf`` usage in all Job files with ``fmt::output_file`` for safer, type-checked file output. diff --git a/docs/newsfragments/+readcon.client.added.md b/docs/newsfragments/+readcon.client.added.md new file mode 100644 index 000000000..aea476cd5 --- /dev/null +++ b/docs/newsfragments/+readcon.client.added.md @@ -0,0 +1 @@ +Add readcon-core v0.4.3 as a meson subproject dependency for C++ con/convel file I/O, replacing the hand-written ``fgets``/``sscanf`` parser. diff --git a/docs/newsfragments/+readcon.client.changed.md b/docs/newsfragments/+readcon.client.changed.md new file mode 100644 index 000000000..788aa165e --- /dev/null +++ b/docs/newsfragments/+readcon.client.changed.md @@ -0,0 +1 @@ +Replace all ``FILE*``-based con/convel I/O in the C++ client (``Matter.cpp``) with readcon-core FFI calls. ``con2matter`` uses mmap-based reading, ``matter2con`` and ``matter2convel`` use the frame builder API. Precision is preserved at 17 decimal places for lossless position roundtrip. diff --git a/docs/newsfragments/+readcon.fileio.changed.md b/docs/newsfragments/+readcon.fileio.changed.md new file mode 100644 index 000000000..03573d621 --- /dev/null +++ b/docs/newsfragments/+readcon.fileio.changed.md @@ -0,0 +1 @@ +Replace custom con/convel parser in ``eon/fileio.py`` with the ``readcon`` package (readcon-core v0.4.3). ``loadcon``, ``loadcons``, and ``savecon`` now delegate to Rust-based parsing and writing, providing identical behavior with better performance on large trajectory files. diff --git a/docs/newsfragments/+uv.dev.changed.md b/docs/newsfragments/+uv.dev.changed.md new file mode 100644 index 000000000..b4d385951 --- /dev/null +++ b/docs/newsfragments/+uv.dev.changed.md @@ -0,0 +1 @@ +Replace PDM with uv for Python dependency management. Development groups are now declared in ``[dependency-groups]`` in ``pyproject.toml`` and locked via ``uv.lock``. From 8fbf4ef20867de47abce8f706dca92a4ac22f6c1 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 20:23:21 +0100 Subject: [PATCH 21/22] fix(ci): docs use .venv/bin/sphinx-build, update readcon-core wrap Docs CI: uv run --no-project could not find sphinx-build in the path. Use .venv/bin/sphinx-build directly since uv sync installs it there. readcon-core wrap: updated to 3b80468 which fixes Windows builds by installing the cargo custom_target (avoiding link_whole promotion error) and using python for cross-platform cargo build commands. --- .github/workflows/ci_docs.yml | 2 +- subprojects/readcon-core.wrap | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml index 94825d307..c302d306d 100644 --- a/.github/workflows/ci_docs.yml +++ b/.github/workflows/ci_docs.yml @@ -42,7 +42,7 @@ jobs: PYTHONPATH: ${{ github.workspace }} run: | uv sync --group docs --no-install-project - uv run --no-project sphinx-build -b html docs/source docs/build/html + .venv/bin/sphinx-build -b html docs/source docs/build/html - name: Upload artifact uses: actions/upload-artifact@v4 diff --git a/subprojects/readcon-core.wrap b/subprojects/readcon-core.wrap index b8fd9036b..e1782f13c 100644 --- a/subprojects/readcon-core.wrap +++ b/subprojects/readcon-core.wrap @@ -1,7 +1,7 @@ [wrap-git] directory = readcon-core url = https://github.com/lode-org/readcon-core.git -revision = d797dc3c185b2d0ceb7bf37b06c6d63749c9fdb1 +revision = 3b80468fdb42384f0eeb880e204d6acf0147eb37 depth = 1 [provide] From 5531731fc3c3c4c8bd79c4685854f20a97559e19 Mon Sep 17 00:00:00 2001 From: Rohit Goswami Date: Tue, 24 Feb 2026 20:44:21 +0100 Subject: [PATCH 22/22] fix(ci): partial_dependency for readcon, pixi-native docs build Three fixes for Windows and docs CI failures: 1. client/meson.build: use partial_dependency() to give eonclib only compile-time readcon headers. The full link dep goes to executables and eclib_dep. Prevents Meson from promoting link_with to link_whole on the cargo custom_target (which is unsupported). 2. ci_docs.yml: replace uv sync + PYTHONPATH approach with a pixi makedocs task. Sphinx and all extensions are now pypi-dependencies in the docs feature, eliminating the need for uv in the docs CI. 3. readcon-core.wrap: update to a8617119 which removes install: true from the cargo custom_target (the other half of the Windows fix). --- .github/workflows/ci_docs.yml | 11 +- pixi.lock | 961 +++++++++++++++++++++++++++++++++- pixi.toml | 23 +- subprojects/readcon-core.wrap | 2 +- 4 files changed, 981 insertions(+), 16 deletions(-) diff --git a/.github/workflows/ci_docs.yml b/.github/workflows/ci_docs.yml index c302d306d..a7b03108d 100644 --- a/.github/workflows/ci_docs.yml +++ b/.github/workflows/ci_docs.yml @@ -29,20 +29,11 @@ jobs: with: cache: true cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }} - activate-environment: true environments: >- docs - - name: Install uv - uses: astral-sh/setup-uv@v6 - - name: Generate Docs - shell: pixi run bash -e {0} - env: - PYTHONPATH: ${{ github.workspace }} - run: | - uv sync --group docs --no-install-project - 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