modify the name

Author: luowh35

doc/gpumd/input_parameters/ensemble_qtb.rst

@@ -0,0 +1,111 @@
+.. _kw_ensemble_qtb:
+.. index::
+   single: nvt_qtb (keyword in run.in)
+   single: npt_qtb (keyword in run.in)
+   single: Quantum Thermal Bath
+
+:attr:`ensemble` (QTB)
+======================
+
+The variants of the :attr:`ensemble` keyword described on this page implement the Quantum Thermal Bath (QTB) method [Dammak2009]_.
+The QTB thermostat is a Langevin-type thermostat that uses colored noise with a quantum Bose-Einstein energy spectrum instead of classical white noise.
+This allows approximate inclusion of nuclear quantum effects (zero-point energy and quantum heat capacity) in otherwise classical MD simulations.
+
+The :attr:`npt_qtb` variant combines the QTB thermostat with the Parrinello-Rahman (MTTK) barostat [Martyna1994]_, equivalent to LAMMPS ``fix nph`` + ``fix qtb``.
+
+
+Syntax
+------
+
+:attr:`nvt_qtb`
+^^^^^^^^^^^^^^^
+
+Run an NVT simulation with the QTB thermostat::
+
+    ensemble nvt_qtb <T_1> <T_2> <T_coup> [f_max <value>] [N_f <value>] [seed <value>]
+
+* :attr:`<T_1>` and :attr:`<T_2>`: Initial and final target temperature (K). The target temperature varies linearly during the run.
+* :attr:`<T_coup>`: Thermostat coupling parameter (in units of timestep). Controls the friction coefficient: :math:`\gamma = 1 / (\text{T\_coup} \times dt)`.
+* :attr:`f_max`: (Optional, default 200) Maximum frequency of the QTB filter in ps\ :sup:`-1`. Should be larger than the highest phonon frequency in the system.
+* :attr:`N_f`: (Optional, default 100) Number of frequency points in the filter. The filter uses :math:`2 N_f` points total.
+* :attr:`seed`: (Optional, default 880302) Random number seed for the colored noise generator.
+
+:attr:`npt_qtb`
+^^^^^^^^^^^^^^^
+
+Run an NPT simulation with the QTB thermostat and Parrinello-Rahman (MTTK) barostat::
+
+    ensemble npt_qtb <direction> <p_1> <p_2> temp <T_1> <T_2> tperiod <tau_T> pperiod <tau_p> [f_max <value>] [N_f <value>] [seed <value>]
+
+Pressure control parameters:
+
+* :attr:`<direction>`: One or more of ``iso``, ``aniso``, ``tri``, ``x``, ``y``, ``z``. Same syntax as :ref:`npt_mttk <mttk>`.
+* :attr:`<p_1>` and :attr:`<p_2>`: Initial and final target pressure (GPa).
+
+Temperature and coupling parameters:
+
+* :attr:`temp <T_1> <T_2>`: Initial and final target temperature (K).
+* :attr:`tperiod <tau_T>`: QTB thermostat coupling period (in units of timestep). Controls friction: :math:`\gamma = 1 / (\text{tperiod} \times dt)`.
+* :attr:`pperiod <tau_p>`: Barostat coupling period (in units of timestep, must be :math:`\geq 200`).
+
+QTB-specific optional parameters (same as :attr:`nvt_qtb`):
+
+* :attr:`f_max`: Maximum frequency (ps\ :sup:`-1`, default 200).
+* :attr:`N_f`: Number of frequency points (default 100).
+* :attr:`seed`: Random seed (default 880302).
+
+
+Examples
+--------
+
+NVT-QTB
+^^^^^^^^
+
+.. code-block:: rst
+
+    ensemble nvt_qtb 300 300 100
+
+Run at 300 K with QTB thermostat. The coupling parameter is 100 timesteps.
+
+.. code-block:: rst
+
+    ensemble nvt_qtb 300 300 100 f_max 150 N_f 200
+
+Same as above but with custom filter parameters.
+
+NPT-QTB
+^^^^^^^^
+
+.. code-block:: rst
+
+    ensemble npt_qtb iso 0 0 temp 300 300 tperiod 100 pperiod 1000
+
+Run at 300 K and 0 GPa with isotropic pressure control.
+
+.. code-block:: rst
+
+    ensemble npt_qtb aniso 0 0 temp 300 300 tperiod 100 pperiod 1000 f_max 200 N_f 100 seed 12345
+
+Anisotropic pressure control with explicit QTB parameters.
+
+.. code-block:: rst
+
+    ensemble npt_qtb x 5 5 y 0 0 z 0 0 temp 300 300 tperiod 100 pperiod 1000
+
+Apply 5 GPa along x and 0 GPa along y and z.
+
+
+Notes
+-----
+
+* The QTB method generates colored noise whose power spectrum matches the quantum energy distribution :math:`E(\omega) = \hbar\omega[\frac{1}{2} + n_{BE}(\omega, T)]`, where :math:`n_{BE}` is the Bose-Einstein distribution.
+* The kinetic temperature reported in ``thermo.out`` will be higher than the target temperature due to zero-point energy contributions. This is expected behavior.
+* For liquid water at 300 K, the kinetic temperature is typically around 1000-1100 K.
+* The :attr:`npt_qtb` ensemble uses the MTTK (Martyna-Tuckerman-Tobias-Klein) integrator for pressure control, which is the same as :ref:`npt_mttk <mttk>` but with the Nosé-Hoover chain thermostat replaced by the QTB thermostat.
+* The :attr:`f_max` parameter should be set larger than the highest phonon frequency in the system. For water, 200 ps\ :sup:`-1` is sufficient.
+
+
+References
+----------
+
+.. [Dammak2009] H. Dammak, Y. Chalopin, M. Laroche, M. Hayoun, and J.-J. Greffet, *Quantum Thermal Bath for Molecular Dynamics Simulation*, Phys. Rev. Lett. **103**, 190601 (2009).

doc/gpumd/input_parameters/ensemble_standard.rst

@@ -44,32 +44,6 @@ If the first parameter is :attr:`nvt_lan`, it is similar to the case of :attr:`n
 ^^^^^^^^^^^^^^^
 If the first parameter is :attr:`nvt_bao`, it is similar to the case of :attr:`nvt_ber`, but using the Langevin method with BAOAB splitting [Leimkuhler2013]_.
 
-:attr:`nvt_qtb`
-^^^^^^^^^^^^^^^
-If the first parameter is :attr:`nvt_qtb`, it is similar to the case of :attr:`nvt_lan`, but using a :term:`QTB` (quantum thermal bath) thermostat with colored noise as proposed by Dammak et al. (Phys. Rev. Lett. 103, 190601, 2009).
-The required parameters are identical to those of :attr:`nvt_lan`::
-
-    ensemble nvt_qtb <T_1> <T_2> <T_coup>
-
-Optional key-value parameters can be appended in any order::
-
-    f_max <f_max> N_f <N_f> seed <seed>
-
-- :attr:`f_max`: frequency cutoff for the colored noise spectrum, in :math:`\mathrm{ps}^{-1}` (default: ``200``)
-- :attr:`N_f`: number of frequency grid points used in the filter construction (default: ``100``)
-- :attr:`seed`: random seed (default: ``880302``)
-
-:attr:`npt_qtb`
-^^^^^^^^^^^^^^^
-If the first parameter is :attr:`npt_qtb`, it combines the :term:`QTB` thermostat with a Berendsen barostat for NPT simulations with nuclear quantum effects.
-This is equivalent to using ``fix nph`` + ``fix qtb`` in LAMMPS.
-The format is::
-
-  ensemble npt_qtb <T_1> <T_2> <T_coup> {<pressure_control_parameters>} [f_max <f_max>] [N_f <N_f>] [seed <seed>]
-
-The pressure control parameters are identical to those of :attr:`npt_ber` (isotropic, orthogonal, or triclinic).
-The optional QTB key-value parameters (:attr:`f_max`, :attr:`N_f`, :attr:`seed`) can be appended after the pressure coupling constant.
-
 :attr:`npt_ber`
 ^^^^^^^^^^^^^^^
 If the first parameter is :attr:`npt_ber`, it means that the ensemble for the current run is NPT (isothermal–isobaric) generated by using the :ref:`Berendsen barostat <berendsen_barostat>`.

doc/gpumd/input_parameters/index.rst

@@ -23,6 +23,7 @@ Below you can find a listing of keywords for the ``run.in`` input file.
    ensemble
    ensemble_standard
    ensemble_mttk
+   ensemble_qtb
    ensemble_heat
    ensemble_pimd
    ensemble_ti_liquid

src/integrate/ensemble_nph_qtb.cu src/integrate/ensemble_npt_qtb.cusrc/integrate/ensemble_nph_qtb.cu renamed to src/integrate/ensemble_npt_qtb.cu

@@ -14,13 +14,13 @@
 */
 
 /*----------------------------------------------------------------------------80
-NPH + QTB: Parrinello-Rahman barostat (MTTK) with QTB colored noise thermostat.
+NPT-QTB: Parrinello-Rahman barostat (MTTK) with QTB colored noise thermostat.
 Equivalent to LAMMPS fix nph + fix qtb.
 [1] Dammak, T., et al. Phys. Rev. Lett. 103, 190601 (2009).
 [2] Martyna, G. J., et al. J. Chem. Phys. 101, 4177 (1994).
 ------------------------------------------------------------------------------*/
 
-#include "ensemble_nph_qtb.cuh"
+#include "ensemble_npt_qtb.cuh"
 #include "langevin_utilities.cuh"
 #include "utilities/common.cuh"
 #include "utilities/gpu_macro.cuh"
@@ -96,7 +96,7 @@ static __global__ void gpu_apply_qtb_half_step(
 
 /* PLACEHOLDER_CONSTRUCTOR */
 
-Ensemble_NPH_QTB::Ensemble_NPH_QTB(const char** params, int num_params)
+Ensemble_NPT_QTB::Ensemble_NPT_QTB(const char** params, int num_params)
 {
   // Initialize MTTK matrices to zero (same as parent constructor)
   for (int i = 0; i < 3; i++) {
@@ -110,7 +110,7 @@ Ensemble_NPH_QTB::Ensemble_NPH_QTB(const char** params, int num_params)
     }
   }
 
-  // NPH + QTB: barostat on, NHC thermostat off (QTB replaces it)
+  // NPT-QTB: barostat on, NHC thermostat off (QTB replaces it)
   ensemble_type = NPH;
   use_barostat = true;
   use_thermostat = false;
@@ -120,8 +120,8 @@ Ensemble_NPH_QTB::Ensemble_NPH_QTB(const char** params, int num_params)
   int qtb_n_f_input = 100;
   qtb_seed = 880302;
 
-  // Parse parameters: nph_qtb <pressure_args> temp <T1> <T2> tperiod <tp> [f_max ...] [N_f ...] [seed ...]
-  int i = 2; // skip "ensemble" and "nph_qtb"
+  // Parse parameters: npt_qtb <pressure_args> temp <T1> <T2> tperiod <tp> [f_max ...] [N_f ...] [seed ...]
+  int i = 2; // skip "ensemble" and "npt_qtb"
   while (i < num_params) {
     if (strcmp(params[i], "iso") == 0 || strcmp(params[i], "aniso") == 0 ||
         strcmp(params[i], "tri") == 0) {
@@ -179,19 +179,19 @@ Ensemble_NPH_QTB::Ensemble_NPH_QTB(const char** params, int num_params)
       if (!is_valid_int(params[i + 1], &qtb_seed)) PRINT_INPUT_ERROR("seed should be an integer.");
       i += 2;
     } else {
-      PRINT_INPUT_ERROR("Unknown nph_qtb keyword.");
+      PRINT_INPUT_ERROR("Unknown npt_qtb keyword.");
     }
   }
 
   if (t_start <= 0 || t_stop <= 0)
-    PRINT_INPUT_ERROR("nph_qtb requires temp <T_start> <T_stop>.");
+    PRINT_INPUT_ERROR("npt_qtb requires temp <T_start> <T_stop>.");
   if (!use_barostat)
-    PRINT_INPUT_ERROR("nph_qtb requires pressure specification (iso/aniso/tri/x/y/z).");
+    PRINT_INPUT_ERROR("npt_qtb requires pressure specification (iso/aniso/tri/x/y/z).");
 
   qtb_N_f = qtb_n_f_input;
 
   // Print summary
-  printf("Use NPH + QTB ensemble for this run.\n");
+  printf("Use NPT-QTB ensemble for this run.\n");
   printf("    Parrinello-Rahman barostat + quantum thermal bath thermostat.\n");
   printf("    QTB temperature: t_start=%g K, t_stop=%g K\n", t_start, t_stop);
   printf("    QTB tperiod=%g timesteps\n", t_period);
@@ -204,19 +204,19 @@ Ensemble_NPH_QTB::Ensemble_NPH_QTB(const char** params, int num_params)
         printf("    %s: p_start=%g, p_stop=%g, pperiod=%g\n", sc[a][b], p_start[a][b], p_stop[a][b], p_period[a][b]);
 }
 
-Ensemble_NPH_QTB::~Ensemble_NPH_QTB(void) {}
+Ensemble_NPT_QTB::~Ensemble_NPT_QTB(void) {}
 
 /* PLACEHOLDER_INIT */
 
-void Ensemble_NPH_QTB::init_mttk()
+void Ensemble_NPT_QTB::init_mttk()
 {
   // Call parent init for barostat setup
   Ensemble_MTTK::init_mttk();
   // Then initialize QTB
   init_qtb();
 }
 
-void Ensemble_NPH_QTB::init_qtb()
+void Ensemble_NPT_QTB::init_qtb()
 {
   qtb_number_of_atoms = atom->number_of_atoms;
   qtb_dt = time_step;
@@ -251,12 +251,12 @@ void Ensemble_NPH_QTB::init_qtb()
   GPU_CHECK_KERNEL
 }
 
-void Ensemble_NPH_QTB::get_target_temp()
+void Ensemble_NPT_QTB::get_target_temp()
 {
   t_target = t_start + (t_stop - t_start) * get_delta();
 }
 
-void Ensemble_NPH_QTB::qtb_update_time_filter(const double target_temperature)
+void Ensemble_NPT_QTB::qtb_update_time_filter(const double target_temperature)
 {
   if (fabs(target_temperature - qtb_last_filter_temperature) < 1.0e-12)
     return;
@@ -289,7 +289,7 @@ void Ensemble_NPH_QTB::qtb_update_time_filter(const double target_temperature)
   qtb_last_filter_temperature = target_temperature;
 }
 
-void Ensemble_NPH_QTB::qtb_refresh_colored_random_force()
+void Ensemble_NPT_QTB::qtb_refresh_colored_random_force()
 {
   const double g3p = sqrt(2.0 * qtb_fric_coef * 12.0 / qtb_h_timestep);
   gpu_refresh_qtb_random_force<<<(qtb_number_of_atoms - 1) / 128 + 1, 128>>>(
@@ -301,7 +301,7 @@ void Ensemble_NPH_QTB::qtb_refresh_colored_random_force()
   GPU_CHECK_KERNEL
 }
 
-void Ensemble_NPH_QTB::qtb_apply_half_step()
+void Ensemble_NPT_QTB::qtb_apply_half_step()
 {
   const int N = qtb_number_of_atoms;
   const double dt_half = 0.5 * qtb_dt;
@@ -334,7 +334,7 @@ void Ensemble_NPH_QTB::qtb_apply_half_step()
 // compute1: press_chain -> QTB_half_kick -> barostat_v -> verlet_v -> box -> verlet_x -> box
 // compute2: verlet_v -> barostat_v -> omega_dot -> QTB_half_kick -> press_chain -> thermo
 
-void Ensemble_NPH_QTB::compute1(
+void Ensemble_NPT_QTB::compute1(
   const double time_step,
   const std::vector<Group>& group,
   Box& box,
@@ -375,7 +375,7 @@ void Ensemble_NPH_QTB::compute1(
   propagate_box();
 }
 
-void Ensemble_NPH_QTB::compute2(
+void Ensemble_NPT_QTB::compute2(
   const double time_step,
   const std::vector<Group>& group,
   Box& box,

src/integrate/ensemble_nph_qtb.cuh src/integrate/ensemble_npt_qtb.cuhsrc/integrate/ensemble_nph_qtb.cuh renamed to src/integrate/ensemble_npt_qtb.cuh

@@ -24,11 +24,11 @@
   #include <curand_kernel.h>
 #endif
 
-class Ensemble_NPH_QTB : public Ensemble_MTTK
+class Ensemble_NPT_QTB : public Ensemble_MTTK
 {
 public:
-  Ensemble_NPH_QTB(const char** params, int num_params);
-  virtual ~Ensemble_NPH_QTB(void);
+  Ensemble_NPT_QTB(const char** params, int num_params);
+  virtual ~Ensemble_NPT_QTB(void);
 
   virtual void compute1(
     const double time_step,