update doxygen comments

.gitignore

@@ -54,5 +54,10 @@ dkms.conf
 # Machine-specific Configuration File
 make.sys
 
+.idea/
+.vscode/
+cmake-build-debug/
+.DS_Store
+
 # Build Output
 build/

src/ChainLattice.c

@@ -29,9 +29,36 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 /**
 @brief Setup a Hamiltonian for the Hubbard model on a Chain lattice
 @author Mitsuaki Kawamura (The University of Tokyo)
+
+@details This function sets up the Hamiltonian for a 1D chain lattice model.
+It handles three different model types:
+- Spin model
+- Hubbard model 
+- Kondo model
+
+The function performs the following steps:
+1. Computes super-cell shape and sites
+2. Validates and stores Hamiltonian parameters
+3. Sets local spin flags and number of sites
+4. Allocates memory for interactions
+5. Sets up transfers and interactions between sites
+
+@param[in,out] StdI Pointer to structure containing model parameters and lattice information
+
+@note The function supports:
+- Nearest neighbor interactions (J0, t0, V0)
+- Second nearest neighbor interactions (J0', t0', V0')  
+- Third nearest neighbor interactions (J0'', t0'', V0'')
+- Local terms (magnetic field h, anisotropy Gamma)
+- On-site Coulomb interaction U (for Hubbard model)
+- Kondo coupling J (for Kondo model)
+
+@note The lattice geometry is written to lattice.gp file for visualization
+
+@warning For Kondo model, the number of sites is doubled to account for localized spins
 */
 void StdFace_Chain(
-  struct StdIntList *StdI//!<[inout]
+  struct StdIntList *StdI //!<[inout] Structure containing model parameters and lattice information
 )
 {
   FILE *fp = NULL;
@@ -238,11 +265,29 @@ void StdFace_Chain(
 #endif
   StdFace_PrintGeometry(StdI);
 }/*void StdFace_Chain*/
-
 #if defined(_HPhi)
 /**
 @brief Setup a Hamiltonian for the generalized Heisenberg model on a Chain lattice
 @author Mitsuaki Kawamura (The University of Tokyo)
+
+@details This function sets up a specialized Hamiltonian for the Heisenberg model on a chain lattice
+using the HPhi boost mode. It handles:
+- Magnetic field terms
+- Nearest and next-nearest neighbor interactions
+- Specialized 6-spin interactions
+
+The function performs:
+1. Sets up unit cell and lattice parameters
+2. Writes magnetic field configuration
+3. Writes interaction parameters
+4. Sets up topology and pivot sites
+5. Configures 6-spin interaction lists
+
+@param[in,out] StdI Pointer to structure containing model parameters
+
+@warning 
+- S2 must be 1 in Boost mode
+- L must be divisible by 8
 */
 void StdFace_Chain_Boost(struct StdIntList *StdI)
 {
@@ -327,6 +372,17 @@ void StdFace_Chain_Boost(struct StdIntList *StdI)
     }
   }
 
+  /*
+   * Initialize the list_6spin_pair array which defines the spin interactions
+   * For each pivot point:
+   * - First 6 rows (indices 0-5) specify which spins are involved in each interaction
+   * - Last row (index 6) specifies the type of interaction (1 or 2)
+   * - Each column represents one interaction, with 8 total interactions per pivot
+   * 
+   * The interactions are arranged in groups:
+   * - Interactions 0-3: Type 1 interactions between adjacent spins
+   * - Interactions 4-7: Type 2 interactions between next-nearest neighbors
+   */
   for (ipivot = 0; ipivot < StdI->num_pivot; ipivot++) {
     StdI->list_6spin_pair[ipivot][0][0] = 0;
     StdI->list_6spin_pair[ipivot][1][0] = 1;

src/FCOrtho.c

@@ -27,9 +27,24 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <string.h>
 
 /**
-@brief Setup a Hamiltonian for the Face-Centered Orthorhombic lattice
-@author Mitsuaki Kawamura (The University of Tokyo)
-*/
+ * @brief Setup a Hamiltonian for the Face-Centered Orthorhombic lattice
+ * @author Mitsuaki Kawamura (The University of Tokyo)
+ * 
+ * This function sets up the Hamiltonian for a face-centered orthorhombic lattice.
+ * The lattice has three primitive vectors:
+ * - W vector: (0, L/2, H/2)
+ * - L vector: (W/2, 0, H/2) 
+ * - H vector: (W/2, L/2, 0)
+ * where W, L, H are the lengths in each direction.
+ *
+ * The function handles three models:
+ * - Spin model: Heisenberg interactions between localized spins
+ * - Hubbard model: Hopping and Coulomb interactions between itinerant electrons
+ * - Kondo model: Coupling between localized spins and itinerant electrons
+ *
+ * @param StdI [inout] Structure containing model parameters and lattice information
+ *                     Modified to store the complete Hamiltonian definition
+ */
 void StdFace_FCOrtho(
   struct StdIntList *StdI//!<[inout]
 )
@@ -40,9 +55,14 @@ void StdFace_FCOrtho(
   double complex Cphase;
   double dR[3];
 
-  /**@brief
-  (1) Compute the shape of the super-cell and sites in the super-cell
-  */
+  /**
+   * @brief Step 1: Compute the shape of the super-cell and sites in the super-cell
+   *
+   * - Opens XSF file for visualization
+   * - Sets number of sites per unit cell (1 for FCO)
+   * - Defines lattice parameters and primitive vectors
+   * - Initializes site positions
+   */
   fp = fopen("lattice.xsf", "w");
   /**/
   StdI->NsiteUC = 1;
@@ -69,9 +89,14 @@ void StdFace_FCOrtho(
   /**/
   StdFace_InitSite(StdI, fp, 3);
   StdI->tau[0][0] = 0.0; StdI->tau[0][1] = 0.0; ; StdI->tau[0][2] = 0.0;
-  /**@brief
-  (2) check & store parameters of Hamiltonian
-  */
+  /**
+   * @brief Step 2: Check and store Hamiltonian parameters
+   *
+   * Handles different parameters depending on model type:
+   * - Spin model: J (exchange), D (anisotropy), magnetic field
+   * - Hubbard model: t (hopping), U (on-site), V (inter-site)
+   * - Kondo model: Combination of spin and Hubbard parameters
+   */
   fprintf(stdout, "\n  @ Hamiltonian \n\n");
   StdFace_NotUsed_d("K", StdI->K);
   StdFace_PrintVal_d("h", &StdI->h, 0.0);
@@ -143,10 +168,13 @@ void StdFace_FCOrtho(
 
   }/*if (model != "spin")*/
   fprintf(stdout, "\n  @ Numerical conditions\n\n");
-  /**@brief
-  (3) Set local spin flag (StdIntList::locspinflag) and
-  the number of sites (StdIntList::nsite)
-  */
+  /**
+   * @brief Step 3: Set local spin flags and number of sites
+   *
+   * - Calculates total number of sites
+   * - Allocates and initializes local spin flags array
+   * - Handles different site counts for Kondo model
+   */
   StdI->nsite = StdI->NsiteUC * StdI->NCell;
   if (strcmp(StdI->model, "kondo") == 0 ) StdI->nsite *= 2;
   StdI->locspinflag = (int *)malloc(sizeof(int) * StdI->nsite);
@@ -160,9 +188,14 @@ void StdFace_FCOrtho(
       StdI->locspinflag[iL] = StdI->S2;
       StdI->locspinflag[iL + StdI->nsite / 2] = 0;
     }
-  /**@brief
-  (4) Compute the upper limit of the number of Transfer & Interaction and malloc them.
-  */
+  /**
+   * @brief Step 4: Calculate memory requirements and allocate arrays
+   *
+   * Computes upper bounds for:
+   * - Number of transfer terms (hopping/field terms)
+   * - Number of interaction terms (exchange/Coulomb terms)
+   * Different calculations done for each model type
+   */
   if (strcmp(StdI->model, "spin") == 0 ) {
     ntransMax = StdI->nsite * (StdI->S2 + 1/*h*/ + 2 * StdI->S2/*Gamma*/);
     nintrMax = StdI->NCell * (StdI->NsiteUC/*D*/ + 6/*J*/ + 3/*J'*/ + 0/*J''*/)
@@ -179,9 +212,15 @@ void StdFace_FCOrtho(
   }
   /**/
   StdFace_MallocInteractions(StdI, ntransMax, nintrMax);
-  /**@brief
-  (5) Set Transfer & Interaction
-  */
+  /**
+   * @brief Step 5: Set up all interactions in the Hamiltonian
+   *
+   * Loops over all unit cells and sets up:
+   * - Local terms (on-site U, magnetic field)
+   * - Nearest neighbor terms along W, L, H directions
+   * - Second nearest neighbor terms
+   * Different terms added depending on model type
+   */
   for (kCell = 0; kCell < StdI->NCell; kCell++){
     /**/
     iW = StdI->Cell[kCell][0];

src/HoneycombLattice.c

@@ -1,23 +1,35 @@
-/*
-HPhi-mVMC-StdFace - Common input generator
-Copyright (C) 2015 The University of Tokyo
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
+/**
+ * @file HoneycombLattice.c
+ * @brief Implementation of the honeycomb lattice model
+ * @copyright Copyright (C) 2015 The University of Tokyo
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
 
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
-/**@file
-@brief Standard mode for the honeycomb lattice
-*/
+/**
+ * @brief Standard mode for the honeycomb lattice
+ * @details This file implements the honeycomb lattice model with various interactions:
+ * - Hubbard model
+ * - Heisenberg model
+ * - Kondo lattice model
+ * The lattice has 2 sites per unit cell and supports:
+ * - Nearest neighbor hopping/exchange
+ * - Next nearest neighbor hopping/exchange
+ * - Third nearest neighbor hopping/exchange
+ * - On-site Coulomb interaction
+ * - Magnetic field
+ */
 #include "StdFace_vals.h"
 #include "StdFace_ModelUtil.h"
 #include <stdlib.h>
@@ -27,9 +39,17 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <string.h>
 
 /**
-@brief Setup a Hamiltonian for the Hubbard model on a Honeycomb lattice
-@author Mitsuaki Kawamura (The University of Tokyo)
-*/
+ * @brief Setup a Hamiltonian for the Hubbard/Heisenberg/Kondo model on a Honeycomb lattice
+ * @details This function:
+ * 1. Computes the shape of the super-cell and sites in the super-cell
+ * 2. Checks & stores parameters of the Hamiltonian
+ * 3. Sets local spin flags and number of sites
+ * 4. Computes upper limits for transfers and interactions
+ * 5. Sets up transfers and interactions between sites
+ *
+ * @param[in,out] StdI Pointer to structure containing model parameters
+ * @author Mitsuaki Kawamura (The University of Tokyo)
+ */
 void StdFace_Honeycomb(struct StdIntList *StdI)
 {
   int isite, jsite, kCell, ntransMax, nintrMax;
@@ -38,9 +58,13 @@ void StdFace_Honeycomb(struct StdIntList *StdI)
   double complex Cphase;
   double dR[3];
 
-  /**@brief
-  (1) Compute the shape of the super-cell and sites in the super-cell
-  */
+  /**
+   * @brief (1) Compute the shape of the super-cell and sites in the super-cell
+   * @details Sets up:
+   * - Lattice vectors
+   * - Unit cell with 2 sites
+   * - Site positions within unit cell
+   */
 #ifdef _HWAVE
   if (StdI->lattice_gp == 1)
 #endif
@@ -64,9 +88,16 @@ void StdFace_Honeycomb(struct StdIntList *StdI)
   StdFace_InitSite(StdI, fp, 2);
   StdI->tau[0][0] = 0.0; StdI->tau[0][1] = 0.0; StdI->tau[0][2] = 0.0;
   StdI->tau[1][0] = 1.0 / 3.0; StdI->tau[1][1] = 1.0 / 3.0; StdI->tau[1][2] = 0.0;
-  /**@brief
-  (2) check & store parameters of Hamiltonian
-  */
+
+  /**
+   * @brief (2) Check & store parameters of Hamiltonian
+   * @details Handles parameters for:
+   * - Magnetic field
+   * - Exchange couplings (spin model)
+   * - Hopping terms (Hubbard model)
+   * - On-site Coulomb U
+   * - Inter-site Coulomb V
+   */
   fprintf(stdout, "\n  @ Hamiltonian \n\n");
   StdFace_NotUsed_d("K", StdI->K);
   StdFace_PrintVal_d("h", &StdI->h, 0.0);
@@ -145,10 +176,13 @@ void StdFace_Honeycomb(struct StdIntList *StdI)
 
   }/*if (model != "spin")*/
   fprintf(stdout, "\n  @ Numerical conditions\n\n");
-  /**@brief
-  (3) Set local spin flag (StdIntList::locspinflag) and
-  the number of sites (StdIntList::nsite)
-  */
+
+  /**
+   * @brief (3) Set local spin flag and number of sites
+   * @details Sets:
+   * - Total number of sites
+   * - Local spin flags for each site
+   */
   StdI->nsite = StdI->NsiteUC * StdI->NCell;
   if (strcmp(StdI->model, "kondo") == 0 ) StdI->nsite *= 2;
   StdI->locspinflag = (int *)malloc(sizeof(int) * StdI->nsite);
@@ -162,9 +196,14 @@ void StdFace_Honeycomb(struct StdIntList *StdI)
       StdI->locspinflag[iL] = StdI->S2;
       StdI->locspinflag[iL + StdI->nsite / 2] = 0;
     }
-  /**@brief
-  (4) Compute the upper limit of the number of Transfer & Interaction and malloc them.
-  */
+
+  /**
+   * @brief (4) Compute upper limit of Transfer & Interaction and malloc them
+   * @details Calculates maximum number of:
+   * - Transfers (hopping/exchange)
+   * - Interactions (Coulomb/exchange)
+   * And allocates memory accordingly
+   */
   if (strcmp(StdI->model, "spin") == 0 ) {
     ntransMax = StdI->nsite * (StdI->S2 + 1/*h*/ + 2 * StdI->S2/*Gamma*/);
     nintrMax = StdI->NCell * (StdI->NsiteUC/*D*/ + 3/*J*/ + 6/*J'*/ + 3/*J''*/)
@@ -182,9 +221,15 @@ void StdFace_Honeycomb(struct StdIntList *StdI)
   }
   /**/
   StdFace_MallocInteractions(StdI, ntransMax, nintrMax);
-  /**@brief
-  (5) Set Transfer & Interaction
-  */
+
+  /**
+   * @brief (5) Set Transfer & Interaction
+   * @details For each unit cell:
+   * - Sets local terms (chemical potential, magnetic field)
+   * - Sets nearest neighbor terms
+   * - Sets next-nearest neighbor terms  
+   * - Sets third-nearest neighbor terms
+   */
   for (kCell = 0; kCell < StdI->NCell; kCell++) {
     /**/
     iW = StdI->Cell[kCell][0];