docs: update README and PyOQP manuals (#138)

* docs: update README and PyOQP manuals

* docs: leave SOC documentation to SOC PR

---------

Co-authored-by: cheolhochoi <cheolhochoi@ultra.tailbd750b.ts.net>

Author: karmachoi

README.md

@@ -11,6 +11,7 @@ Open Quantum Platform ([OpenQP](https://pubs.acs.org/doi/10.1021/acs.jctc.4c0111
 - **New Exchange-Correlation Functionals** of [**DTCAM** series](https://doi.org/10.1021/acs.jctc.4c00640) for MRSF-TDDFT
 - **Ground State Properties** by HF and DFT theories
 - **Geometry Optimization, Transition State Search, and Conical Intersection Search** by SciPy and [DL-Find](https://github.com/digital-chemistry-laboratory/libdlfind)
+- [geomeTRIC](https://github.com/leeping/geomeTRIC) optimizer backend for state-specific optimization, MECI, MECP, transition-state searches, constrained optimizations, and IRC paths
 - [PyRAI2MD](https://github.com/mlcclab/PyRAI2MD-hiam) Integration to support Artificial Intelligence Ab Initio Molecular Dynamics
 - [LibXC](https://gitlab.com/libxc/libxc) Integration to support a variety of exchange-correlation functionals
 - [basis_set_exchange](https://github.com/MolSSI-BSE/basis_set_exchange) Integration to support a variety of basis sets
@@ -20,6 +21,8 @@ Open Quantum Platform ([OpenQP](https://pubs.acs.org/doi/10.1021/acs.jctc.4c0111
 - **OpenMP and MPI Parallelization** and **BLAS/LAPACK Optimization** for high performance
 - [OpenTrustRegion library](https://github.com/eriksen-lab/opentrustregion) for stable SCF convergence
 - Native PySCF-based advanced initial guesses, plus optional [MOKIT](https://github.com/1234zou/MOKIT) support for broader external wavefunction conversion workflows
+- Native PySCF-backed initial guesses: `guess.type=pyscf`, `guess.type=sad`, and `guess.type=sap`
+- [OpenqpView](https://open-quantum-platform.github.io/OpenqpView/) browser-based visualization for OpenQP outputs, supporting local log, JSON, Molden, cube, and XYZ inspection
 
 ### Upcoming Features
 - **Efficient electrostatic embedding QM/MM** by [ESPF QM/MM](https://doi.org/10.1063/5.0133646)
@@ -132,6 +135,9 @@ For more in-depth information, visit:
 ### Input Generator
 Easily create input files for OpenQP using our [Web-based Input Generator](https://open-quantum-platform.github.io/OpenQP_Input_Generator/).
 
+### OpenqpView
+Inspect OpenQP calculation outputs directly in the browser with [OpenqpView](https://open-quantum-platform.github.io/OpenqpView/). Recent OpenqpView development added a GitHub Pages deployment, full-periodic-table molecule rendering, local file/drop/paste loading, WebGL auto-spin controls, and support for OpenQP log, JSON, Molden, cube, and XYZ data. Files and pasted text are processed locally in the browser and are not uploaded to a server.
+
 ### Citing OpenQP
 If you use OpenQP in your research, please cite the following papers:
 

pyoqp/README.md

@@ -6,6 +6,8 @@
 
 - Geometry optimization for arbitrary state local minimum, MECI, MEP with Scipy library
 - Geometry optimization for arbitrary state local minimum, MECI, TS with DL-FIND library
+- Geometry optimization with geomeTRIC for state-specific optimization, MECI, MECP, TS, constrained optimizations, and IRC paths
+- Native PySCF-backed initial guesses: `pyscf`, `sad`, and `sap`
 - Energy gradient calculations interface for nonadiabatic molecular dynamics
 
 ## Prerequisite
@@ -81,6 +83,18 @@ Results, including log files and `test_report.txt`, will be stored in the curren
     save_mol=False
     continue_geom=False
 
+[geometric]
+    coordsys=tric
+    trust=0.1
+    tmax=0.3
+    convergence_set=GAU
+    prefix=geometric
+    hessian=never
+    irc_direction=forward
+    constraints_file=''
+    enforce=0.0
+    conmethod=0
+
 [scf]
     type=rhf
     maxit=30
@@ -188,6 +202,7 @@ input section handle the basic information of molecular system
       meci       minimum energy conical intersection optimization
       mep        minimum energy path calculation
       ts         transition state optimization
+      irc        intrinsic reaction coordinate with [optimize]lib=geometric
       neb        nudge elasted band calculation (not avaialble yet)
 
 - system // specify molecular structure or xyz file
@@ -217,6 +232,14 @@ guess section handle the guess orbitals
       hcore      hcore guess
       model      read orbital from molden
       json       load data from json
+      auto       load json if the requested file exists; otherwise use huckel
+      pyscf      run a PySCF SCF calculation and import the converged orbitals
+      sad        build a PySCF superposition-of-atomic-density initial guess
+      sap        build a PySCF superposition-of-atomic-potential initial guess
+
+      pyscf, sad, and sap use the native OpenQP JSON restart exporter.
+      PySCF is installed with OpenQP's Python dependencies. MOKIT is not
+      required for these initial guesses.
 
 - file // set the guess orbital or data file
 
@@ -384,6 +407,7 @@ optimize section handle the geometry optimization
 
       scipy       use scipy.optimize library (default)
       dlfind      use DL-FIND library
+      geometric   use geomeTRIC. Supports runtype=optimize, meci, mecp, ts, and irc
 
 - optimizer // choose the scipy optimizer
 
@@ -463,6 +487,52 @@ optimize section handle the geometry optimization
       True       do initial SCF iterations in every optimization step
       False      do not do initial SCF iterations after the first optimization step
 
+### [geometric]
+
+geometric section controls the geomeTRIC optimizer backend when [optimize]lib=geometric
+
+- coordsys // coordinate system passed to geomeTRIC
+
+      tric       translation-rotation internal coordinates (default)
+
+- trust // initial trust radius in Angstrom
+
+      0.1 (default)
+
+- tmax // maximum trust radius in Angstrom
+
+      0.3 (default)
+
+- convergence_set // geomeTRIC convergence preset
+
+      GAU (default)
+
+- prefix // prefix for geomeTRIC output files
+
+      geometric (default)
+
+- hessian // initial Hessian option passed to geomeTRIC
+
+      never (default for minima and constrained optimization)
+      first (recommended/automatically used for ts and irc if hessian=never)
+
+- irc_direction // IRC branch direction for runtype=irc
+
+      forward (default)
+      backward
+
+- constraints_file // geomeTRIC constraints file for constrained optimization
+
+      relative paths are resolved relative to the OpenQP input file
+
+- enforce // geomeTRIC constraint enforcement value
+
+      0.0 (default)
+
+- conmethod // geomeTRIC constraint method
+
+      0 (default)
+
 ### [dlfind]
 
 dlfind section handle the DL-FIND library for geometry optimization