Implement missing source structure for CMakeLists.txt build system

[Copilot]

CMakeLists.txt referenced libraries (vsepr_io, vsepr_thermal, vsepr_api) and source files that didn't exist, causing complete build failure. Entire src/, apps/, and include/ directory structure was missing.

Changes

Directory Structure (23 files, ~1K LOC)

• Created complete src/ hierarchy: core, sim, io, thermal, api, cli, pot, box, nl, int, build, vis
• Created apps/ with entry points: cli.cpp, vsepr-cli, vsepr_batch, xyz_suite_test
• Created include/ with public headers: io_api.h, xyz_format.h, xyzc_format.h

Library Implementations

• vsepr_io: XYZ file format I/O with read/write operations
• vsepr_thermal: XYZC thermal trajectory format with energy transfer tracking
• vsepr_api: C API façade wrapping C++ I/O operations
• spec_parser: Specification parser stub
• vsepr_sim: Simulation engine stub

CLI Commands

• Implemented command routing in apps/cli.cpp
• Created all 7 command handlers: help, version, build, viz, therm, webgl, stream
• Functions currently print TODO messages for unimplemented features

Core Types (src/core/types.hpp)

struct Vec3 {
    double x, y, z;
    Vec3 operator+(const Vec3&) const;
    Vec3 operator-(const Vec3&) const;
    double dot(const Vec3&) const;
};

struct Atom {
    std::string element;
    Vec3 position, velocity, force;
    double mass, charge;
    int id;
};

struct Molecule {
    std::vector<Atom> atoms;
    double energy;
};

Build Status

Builds successfully with -DBUILD_VIS=OFF -DBUILD_TESTS=OFF:

• 5 static libraries compile
• 4 executables link and run
• xyz_suite_test validates I/O operations

Notes

• All implementations are minimal stubs with TODO comments
• BUILD_TESTS=ON requires test source files (not created)
• BUILD_VIS=ON requires ImGui dependencies (not addressed)
• Minor warnings for unused parameters in stub functions

Original prompt

Problem

The CMakeLists.txt file references several libraries and source files that don't exist or aren't properly defined, causing build failures:

Missing Library Definitions

1. vsepr_io - Referenced in line 123 but never defined

   • Used by vsepr_api target (line 123)
   • Used by xyz_suite_test target (line 209)

2. vsepr_thermal - Referenced in line 123 but never defined

   • Used by vsepr_api target (line 123)

3. vsepr_build - Referenced in line 315 (commented out) but never defined

   • Formula builder tests are disabled due to API mismatch

Missing Source Files

The vsepr executable references several CLI command source files that may not exist:

set(VSEPR_SOURCES
    apps/cli.cpp
    src/cli/cmd_help.cpp
    src/cli/cmd_version.cpp
    src/cli/cmd_build.cpp
    src/cli/cmd_viz.cpp
    src/cli/cmd_therm.cpp
    src/cli/cmd_webgl.cpp
    src/cli/cmd_stream.cpp
)

Missing Source File: spec_parser

• src/spec_parser.cpp (line 126) - Used by vsepr_batch but may not exist

Missing API Implementation

• src/api/io_api.cpp (line 120) - Used by vsepr_api but may not exist

Tasks

1. Verify which source files actually exist in the repository
2. Create stub/minimal implementations for missing source files:
   • src/cli/cmd_*.cpp files if they don't exist
   • src/spec_parser.cpp if it doesn't exist
   • src/api/io_api.cpp if it doesn't exist
3. Add missing library definitions to CMakeLists.txt:
   • Define vsepr_io library (I/O operations)
   • Define vsepr_thermal library (thermal analysis)
   • Optionally define vsepr_build library (formula builder)
4. Comment out or fix broken references if files can't be created
5. Ensure the build can complete with -DBUILD_VIS=OFF option

Expected Outcome

After these fixes:

• cmake .. should configure without errors
• cmake --build . should compile successfully (at minimum with -DBUILD_VIS=OFF)
• Basic executables like vsepr-cli, vsepr_batch, and test binaries should build
• Any remaining issues should be documented in comments

Implementation Notes

• Focus on minimal working implementations - stub functions are acceptable
• Preserve existing working code
• Add clear TODO comments for incomplete implementations
• Update CMakeLists.txt to be more resilient (use if(EXISTS ...) checks where appropriate)
• Consider creating header-only libraries for vsepr_io and vsepr_thermal if implementations don't exist

Priority

HIGH - This blocks all C++ development and testing

This pull request was created from Copilot chat.

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