Merge pull request #791 from maki49/develop

Merge `develop` into `TDDFT`

Author: mohanchen

.github/workflows/dynamic.yml

@@ -2,7 +2,7 @@ name: Dynamic Analysis
 
 on:
   schedule:
-    - cron: '0 20 * * *'
+    - cron: '0 3 * * *'
   workflow_dispatch:
     inputs:
       name:
@@ -14,6 +14,7 @@ jobs:
   test:
     name: Do the job on the runner
     runs-on: self-hosted
+    if: github.repository_owner == 'deepmodeling'
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout

.github/workflows/static.yaml

@@ -6,6 +6,7 @@ on:
 jobs:
   clang-tidy:
     runs-on: self-hosted
+    if: github.repository_owner == 'deepmodeling'
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout Pull Request

.github/workflows/test.yml

@@ -4,6 +4,7 @@ on:
   pull_request_target:
     branches:
       - develop
+      - tryEigen
       - update_MD
       - ABACUS_2.2.0_beta
       - deepks
@@ -12,9 +13,11 @@ on:
       - TDDFT
 jobs:
 
+jobs:
   test:
     name: Do the job on the runner
     runs-on: self-hosted
+    if: github.repository_owner == 'deepmodeling'
     container: ghcr.io/deepmodeling/abacus-development-kit:gnu
     steps:
       - name: Checkout

CMakeLists.txt

@@ -225,8 +225,8 @@ IF (BUILD_TESTING)
   enable_testing()
   find_package(Threads)
   set(CMAKE_CXX_STANDARD_REQUIRED ON)
-  find_package(GTest)
-  if(NOT ${GTEST_FOUND})
+  find_package(GTest HINTS /usr/local/lib/ ${GTEST_DIR})
+  if(NOT ${GTest_FOUND})
     include(FetchContent)
     FetchContent_Declare(
       googletest
@@ -260,7 +260,6 @@ target_link_libraries(${ABACUS_BIN_NAME}
     cell
     symmetry
     md
-    symmetry
     neighbor
     orb
     io
@@ -272,6 +271,7 @@ target_link_libraries(${ABACUS_BIN_NAME}
     pw
     ri
     driver
+    xc
     esolver
     -lm
 )

doc/developers.md

@@ -11,9 +11,9 @@
   - [Code Formatting style](#code-formatting-style)
     [back to main page](../README.md)
 
-## Raising issues on GitHub
+## Creating issues on GitHub
 
-Raising issues on GitHub is a convernient way to notify the develper team about bugs and feature requests of the ABACUS code. We provide a few templates for issues.
+Creating issues on GitHub is a convernient way to notify the develper team about bugs and feature requests of the ABACUS code. We provide a few templates for issues.
 
 [back to top](#for-developers)
 
@@ -23,7 +23,7 @@ The ABACUS code is refactored to several self-contained modules. A description o
 
 ### Add a unit test
 
-If there are currently no unit tests provided for the module, do as follows. `module_base` provides a simple demonstration.
+We use GoogleTest as our test framework. Write your test under the corresponding module folder at `abacus-develop/tests`, then append the test to `tests/CMakeLists.txt`. If there are currently no unit tests provided for the module, do as follows. `module_base` provides a simple demonstration.
 
 - Add a folder named `test` under the module.
 - Append the content below to `CMakeLists.txt` of the module:
@@ -106,9 +106,6 @@ After your pull request is merged, you can safely delete your branch and pull th
     git pull --ff upstream develop
     ```
 
-### Providing unit tests
-
-We use GoogleTest as our test framework. Write your test under the corresponding module folder at `abacus-develop/tests`, then append the test to `tests/CMakeLists.txt`. To build tests for abacus, set `BUILD_TESTING=1` when configuring with CMake. Executables of test programs will be under `build/tests`.
 
 ### Updating documentation
 

doc/examples/md.md

@@ -33,24 +33,22 @@ basis_type          lcao
 mixing_beta         0.4
 charge_extrap       second-order
 
-md_mdtype           1    //choose ensemble
+md_type           1    //choose ensemble
 md_dt               1    //time step
 md_tfirst           700  //the first target temperature
-md_rstmd            0    //whether restart md
-md_qmass            1    //mass of themostat
-md_dumpfred       10   //The period to dump MD information for monitoring and restarting MD
+md_restart            0    //whether restart md
+md_dumpfreq       10   //The period to dump MD information
 ```
 
 These MD parameters means that ABACUS will use NVT ensemble with Nosé-hoover themostat; the time step is 1fs, and target temperature is 700K; start renew without restart file, set the mass of themostat as 1g/mol, and calculate the MSD and diffusion coefficent from first step.
 
 Note: *Please turn off symmetry when do MD simulation.*
 
-- md_mdtype : 0, NVE; 1, NVT; 2, velocity scaling
+- md_type : -1, FIRE; 0, NVE; 1, NHC; 2, LGV; 3, ADS; 4, MSST
 - md_dt : time step in md simulation (fs)
-- md_tfirst : target temperature in md simulation(K), you should set parameter md_tlast and md_fixtemperature when you want to change temperature during md simulation.
-- md_rstmd : 0, no need of restart ; 1, restart with restart file, you must repalce STRU file with STRU_MD before you run the restart task.
-- md_qmass : mass of thermostat, set by experience, if you don’t know how to set, set it to 0 will have a number autosetted by ABACUS
-- md_dumpfred : frequency for output consequence of md simulation
+- md_tfirst : target temperature in md simulation(K), you should set parameter md_tlast when you want to change temperature during md simulation.
+- md_restart : 0, no need of restart ; 1, restart with restart file, you must repalce STRU file with STRU_MD before you run the restart task.
+- md_dumpfreq : frequency for output consequence of md simulation
 
 The STRU file is:
 ```
@@ -149,9 +147,9 @@ Gamma
 ```
 
 Run the program, and see results in the output directory. The following files are about MD:
-- md_pos_$num.cif optimized structure in direct coordinate
-- MD_RESTART output the information of md for restart
-- STRU_MD if you want to restart md, you must replace the STRU with this file.
+- STRU_MD_$num: optimized structures in direct coordinate
+- Restart_md.dat: output the information of md for restart
+- If you want to restart md, you must replace the STRU with STRU_MD_$num.
 
 MD information can be found in file running_md.log or in file MD_OUT
 

doc/examples/tddft.md

@@ -25,20 +25,12 @@ out_charge 1
 gamma_only 0
 nstep 2000
 dr2 1.0e-6
-md_mdtype 0
+md_type 0
 md_dt 0.01
 md_tfirst 30
-md_mdoutpath mdtest
-md_rstmd 0
-md_fixtemperature 20000
-md_nresn 3
-md_nyosh 3
-md_qmass 0
+md_restart 0
 md_tlast 30
-md_dumpfred 1
-md_domsd 0
-md_domsdatom 0
-md_outputstressperiod 0
+md_dumpfreq 1
 tddft 1
 set_vel 1
 ocp 1

doc/input-main.md

@@ -32,18 +32,14 @@
     - [Density of states](#density-of-states)
 
         [dos_edelta_ev](#dos-edelta-ev) | [dos_sigma](#dos-sigma) | [dos_scale](#dos-scale)
-
-    - [Electric field](#electric-field)
-    
-        [efield](#efield) | [edir](#edir) | [emaxpos](#emaxpos) | [eopreg](#eopreg) | [eamp](#eamp)
 
     - [Exact exchange](#exact-exchange) (under tests)
 
         [exx_hybrid_type](#exx-hybrid-type) | [exx_hybrid_alpha](#exx-hybrid-alpha) | [exx_hse_omega](#exx-hse-omega) | [exx_separate_loop](#exx-separate-loop) | [exx_hybrid_step](#exx-hybrid-step) | [exx_lambda](#exx-lambda) | [exx_pca_threshold](#exx-pca-threshold) | [exx_c_threshold](#exx-c-threshold) | [exx_v_threshold](#exx-v-threshold) | [exx_dm_threshold](#exx-dm-threshold) | [exx_schwarz_threshold](#exx-schwarz-threshold) | [exx_cauchy_threshold](#exx-cauchy-threshold) | [exx_ccp_threshold](#exx-ccp-threshold) | [exx_ccp_rmesh_times](#exx-ccp-rmesh-times) | [exx_distribute_type](#exx-distribute-type) | [exx_opt_orb_lmax](#exx-opt-orb-lmax) | [exx_opt_orb_ecut](#exx-opt-orb-ecut) | [exx_opt_orb_tolerence](#exx-opt-orb-tolerence)
 
     - [Molecular dynamics](#molecular-dynamics)
 
-        [md_type](#md-type) | [md_potential](#md-potential) | [md_rstmd](#md-rstmd) | [md_dt](#md_dt) | [md_t](#md-t) | [md_qmass](#md-qmass) | [md_dumpfred](#md-dumpfred) | [md_rstfred](#md-rstfred) | [md_tfreq](#md-tfreq) | [MNHC](#mnhc) | [rcut_lj](#rcut_lj) | [epsilon_lj](#epsilon_lj) | [sigma_lj](#sigma_lj) | [direction](#direction) | [velocity](#velocity) | [viscosity](#viscosity) | [tscale](#tscale) | [damp](#damp)
+        [md_type](#md-type) | [md_ensolver](#md-ensolver) | [md_restart](#md-restart) | [md_dt](#md-dt) | [md_t](#md-t) | [md_dumpfreq](#md-dumpfreq) | [md_restartfreq](#md-restartfreq) | [md_tfreq](#md-tfreq) | [md_mnhc](#md-mnhc) | [lj_rcut](#lj-rcut) | [lj_epsilon](#lj-epsilon) | [lj_sigma](#lj-sigma) | [msst_direction](#msst-direction) | [msst_vel](#msst-vel) | [msst_vis](#msst-vis) | [msst_tscale](#msst-tscale) | [msst_qmass](#msst-qmass) | [md_damp](#md-damp)
 
     - [DFT+U correction](#DFT_U-correction)
 
@@ -912,43 +908,6 @@ This part of variables are used to control the calculation of DOS.
 
     [back to top](#input-file)
 
-### Electric field
-This part of variables are used to control the addition of an external electric field. It is achieved by adding a saw-like potential to the local ionic potential.
-
-- efield<a id="efield"></a>
-    - *Type*: Boolean
-    - *Description*: Controls whether to add the external electric field. When set to 1, the electric field is turned on. When set to 0, there is no electric field.
-    - *Default*: 0.
-
-    [back to top](#input-file)
-
-- edir<a id="edir"></a>
-    - *Type*: Integer
-    - *Description*: Tells which reciprocal lattice vector the external electric field aligns with. Allowed values are 1,2, and 3, corresponding to the three reciprocal lattice vectors respectively.
-    - *Default*: 1
-
-    [back to top](#input-file)
-
-- emaxpos<a id="emaxpos"></a>
-    - *Type*: Real
-    - *Description*: Position of the maximum of the saw-like potential along the reciprocal lattice vector specified by edir, 0 < emaxpos < 1.
-    - *Default*: 0.5
-
-    [back to top](#input-file)
-
-- eopreg<a id="eopreg"></a>
-    - *Type*: Real
-    - *Description*: The saw-like potential increases in the region from `(emaxpos+eopreg-1)` to `(emaxpos)`, then decreases to 0 until (emaxpos+eopreg), in units of the crystal vector `edir`. Important: the change of slope of this potential must be located in the empty region, or else unphysical forces will result.
-    - *Default*: 0.1
-
-    [back to top](#input-file)
-
-- eamp<a id="eamp"></a>
-    - *Type*: Real
-    - *Description*: Amplitude of the electric field, in atomic unit: 1 a.u. = 51.4220632*10^10 V/m.
-    - *Default*: 0.001
-
-    [back to top](#input-file)
 
 ### DeePKS
 This part of variables are used to control the usage of DeePKS method (a comprehensive data-driven approach to improve accuracy of DFT).
@@ -1113,61 +1072,56 @@ This part of variables are used to control the molecular dynamics calculations.
     - *Description*: control the ensemble to run md.
         - -1: FIRE method to relax;
         - 0: NVE ensemble;
-        - 1: NVT ensemble with Anderson thermostat;
-        - 2: NVT ensemble with Nose Hoover Chain;
-        - 3: NVT ensemble with Langevin method;
+        - 1: NVT ensemble with Nose Hoover Chain;
+        - 2: NVT ensemble with Langevin method;
+        - 3: NVT ensemble with Anderson thermostat;
         - 4: MSST method; 
-    - *Default*: 2
+    - *Default*: 1
 
     [back to top](#input-file)
 
-- md_potential<a id="md-potential"></a>
+- md_ensolver<a id="md-ensolver"></a>
     - *Type*: String
-    - *Description*: choose the potential type.
+    - *Description*: choose the energy solver for MD.
         - FP: First-Principles MD;
         - LJ: Leonard Jones potential;
         - DP: DeeP potential;
     - *Default*: FP
 
     [back to top](#input-file)
 
-- md_rstmd<a id="md-rstmd"></a>
+- md_restart<a id="md-restart"></a>
     - *Type*: Boolean
     - *Description*: to control whether restart md.
         - 0: When set to 0, ABACUS will calculate md normolly.
         - 1: When set to 1, ABACUS will calculate md from last step in your test before.
     - *Default*: 0
 
     [back to top](#input-file)
-- md_dt<a id="md_dt"></a>
+- md_dt<a id="md-dt"></a>
     - *Type*: Double
     - *Description*: This is the time step(fs) used in md simulation .
     - *Default*: 1
 
     [back to top](#input-file)
 - md_tfirst & md_tlast<a id="md-t"></a>
     - *Type*: Double
-    - *Description*: This is the temperature used in md simulation, md_tlast’s default value is md_tfirst. If md_tlast is setted and be different from the md_tfirst, ABACUS will automatically generate a linear temperature gradient file named ”ChangeTemp.dat”, you can also set this file according to your needs instead.
+    - *Description*: This is the temperature (K) used in md simulation, md_tlast’s default value is md_tfirst. If md_tlast is set to be different from md_tfirst, ABACUS will automatically change the temperature from md_tfirst to md_tlast.
     - *Default*: No default
 
     [back to top](#input-file)
-- md_qmass<a id="md-qmass"></a>
-    - *Type*: Double
-    - *Description*: Inertia of extended system variable. Used only when md_type is 4, you should set a number which is larger than 0. Note that Qmass of NHC is set by md_tfreq.
-    - *Default*: No default
 
-    [back to top](#input-file)
-- md_dumpfred<a id="md-dumpfred"></a>
+- md_dumpfreq<a id="md-dumpfreq"></a>
     - *Type*: Integer
     - *Description*:This is the frequence to dump md information.
     - *Default*: 1
 
     [back to top](#input-file)
 
-- md_rstfred<a id="md-rstfred"></a>
+- md_restartfreq<a id="md-restartfreq"></a>
     - *Type*: Integer
     - *Description*:This is the frequence to output restart information.
-    - *Default*: 1
+    - *Default*: 5
 
     [back to top](#input-file)
 
@@ -1180,63 +1134,70 @@ This part of variables are used to control the molecular dynamics calculations.
 
     [back to top](#input-file)
 
-- MNHC<a id="mnhc"></a>
+- md_mnhc<a id="md-mnhc"></a>
     - *Type*: Integer
     - *Description*: Number of Nose-Hoover chains.
     - *Default*: 4
 
     [back to top](#input-file)
 
-- rcut_lj<a id="rcut_lj"></a>
+- lj_rcut<a id="lj-rcut"></a>
     - *Type*: Real
     - *Description*: Cut-off radius for Leonard Jones potential (angstrom).
     - *Default*: 8.5 (for He)
 
     [back to top](#input-file)
 
-- epsilon_lj<a id="epsilon_lj"></a>
+- lj_epsilon<a id="lj-epsilon"></a>
     - *Type*: Real
     - *Description*: The value of epsilon for Leonard Jones potential (eV).
     - *Default*: 0.01032 (for He)
 
     [back to top](#input-file)
 
-- sigma_lj<a id="sigma_lj"></a>
+- lj_sigma<a id="lj-sigma"></a>
     - *Type*: Real
     - *Description*: The value of sigma for Leonard Jones potential (angstrom).
     - *Default*: 3.405 (for He)
 
     [back to top](#input-file)
 
-- direction<a id="direction"></a>
+- msst_direction<a id="msst-direction"></a>
     - *Type*: Integer
     - *Description*: the direction of shock wave for MSST.
     - *Default*: 2 (z direction)
 
     [back to top](#input-file)
 
-- velocity<a id="velocity"></a>
+- msst_vel<a id="msst-vel"></a>
     - *Type*: Real
     - *Description*: the velocity of shock wave (\AA/fs) for MSST.
     - *Default*: 0
 
     [back to top](#input-file)
 
-- viscosity<a id="viscosity"></a>
+- msst_vis<a id="msst-vis"></a>
     - *Type*: Real
     - *Description*: artificial viscosity (mass/length/time) for MSST.
     - *Default*: 0
 
     [back to top](#input-file)
 
-- tscale<a id="tscale"></a>
+- msst_tscale<a id="msst-tscale"></a>
     - *Type*: Real
     - *Description*: reduction in initial temperature (0~1) used to compress volume in MSST.
     - *Default*: 0
 
     [back to top](#input-file)
 
-- damp<a id="damp"></a>
+- msst_qmass<a id="msst-qmass"></a>
+    - *Type*: Double
+    - *Description*: Inertia of extended system variable. Used only when md_type is 4, you should set a number which is larger than 0. Note that Qmass of NHC is set by md_tfreq.
+    - *Default*: No default
+
+    [back to top](#input-file)
+
+- md_damp<a id="md-damp"></a>
     - *Type*: Real
     - *Description*: damping parameter (fs) used to add force in Langevin method.
     - *Default*: 1