Refactor: rename some MD input parameters (#2012)

YuLiu98 · web-flow · commit bd6244b5745a · 2023-03-08T18:25:14.000+08:00
diff --git a/docs/advanced/input_files/input-main.md b/docs/advanced/input_files/input-main.md
@@ -32,7 +32,7 @@
   [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_c_grad_threshold](#exx_c_grad_threshold) | [exx_v_grad_threshold](#exx_v_grad_threshold) | [exx_dm_threshold](#exx_dm_threshold) | [exx_schwarz_threshold](#exx_schwarz_threshold) | [exx_cauchy_threshold](#exx_cauchy_threshold) | [exx_cauchy_grad_threshold](#exx_cauchy_grad_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) | [exx_real_number](#exx_real_number)
 - [Molecular dynamics](#molecular-dynamics)
 
-  [md_type](#md_type) | [md_thermostat](#md_thermostat) | [md_nstep](#md_nstep) | [md_restart](#md_restart) | [md_dt](#md_dt) | [md_tfirst, md_tlast](#md_tfirst-md_tlast) | [md_dumpfreq](#md_dumpfreq) | [md_restartfreq](#md_restartfreq) | [md_seed](#md_seed) | [md_tfreq](#md_tfreq) | [md_tchain](#md_tchain) | [md_pmode](#md_pmode) | [md_pcouple](#md_pcouple) | [md_pfirst, md_plast](#md_pfirst-md_plast) | [md_pfreq](#md_pfreq) | [md_pchain](#md_pchain) | [out_force](#out_force) | [out_vel](#out_vel) | [out_virial](#out_virial) | [lj_rcut](#lj_rcut) | [lj_epsilon](#lj_epsilon) | [lj_sigma](#lj_sigma) | [pot_file](#pot_file) | [msst_direction](#msst_direction) | [msst_vel](#msst_vel) | [msst_vis](#msst_vis) | [msst_tscale](#msst_tscale) | [msst_qmass](#msst_qmass) | [md_damp](#md_damp) | [md_tolerance](#md_tolerance) | [md_nraise](#md_nraise)
+  [md_type](#md_type) | [md_thermostat](#md_thermostat) | [md_nstep](#md_nstep) | [md_restart](#md_restart) | [md_dt](#md_dt) | [md_tfirst, md_tlast](#md_tfirst-md_tlast) | [md_dumpfreq](#md_dumpfreq) | [md_restartfreq](#md_restartfreq) | [md_seed](#md_seed) | [md_tfreq](#md_tfreq) | [md_tchain](#md_tchain) | [md_pmode](#md_pmode) | [md_pcouple](#md_pcouple) | [md_pfirst, md_plast](#md_pfirst-md_plast) | [md_pfreq](#md_pfreq) | [md_pchain](#md_pchain) | [dump_force](#dump_force) | [dump_vel](#dump_vel) | [dump_virial](#dump_virial) | [lj_rcut](#lj_rcut) | [lj_epsilon](#lj_epsilon) | [lj_sigma](#lj_sigma) | [pot_file](#pot_file) | [msst_direction](#msst_direction) | [msst_vel](#msst_vel) | [msst_vis](#msst_vis) | [msst_tscale](#msst_tscale) | [msst_qmass](#msst_qmass) | [md_damp](#md_damp) | [md_tolerance](#md_tolerance) | [md_nraise](#md_nraise)
 - [vdW correction](#vdw-correction)
 
   [vdw_method](#vdw_method) | [vdw_s6](#vdw_s6) | [vdw_s8](#vdw_s8) | [vdw_a1](#vdw_a1) | [vdw_a2](#vdw_a2) | [vdw_d](#vdw_d) | [vdw_abc](#vdw_abc) | [vdw_C6_file](#vdw_c6_file) | [vdw_C6_unit](#vdw_c6_unit) | [vdw_R0_file](#vdw_r0_file) | [vdw_R0_unit](#vdw_r0_unit) | [vdw_cutoff_type](#vdw_cutoff_type) | [vdw_cutoff_radius](#vdw_cutoff_radius) | [vdw_radius_unit](#vdw_radius_unit) | [vdw_cutoff_period](#vdw_cutoff_period) | [vdw_cn_thr](#vdw_cn_thr) | [vdw_cn_thr_unit](#vdw_cn_thr_unit)
@@ -1662,19 +1662,19 @@ These variables are used to control the molecular dynamics calculations.
 - **Description**: number of thermostats coupled with the barostat in the Nose Hoover Chain method.
 - **Default**: 1
 
-### out_force
+### dump_force
 
 - **Type**: Boolean
 - **Description**: Output atomic forces into the file `MD_dump` or not. If `true`, forces will be written, otherwise forces will not be written.
 - **Default**: false
 
-### out_vel
+### dump_vel
 
 - **Type**: Boolean
 - **Description**: Output atomic velocities into the file `MD_dump` or not. If `true`, velocities will be written, otherwise velocities will not be written.
 - **Default**: false
 
-### out_virial
+### dump_virial
 
 - **Type**: Boolean
 - **Description**: Output lattice virial into the file `MD_dump` or not. If `true`, lattice virial will be written, otherwise lattice virial will not be written.
diff --git a/docs/advanced/md.md b/docs/advanced/md.md
@@ -30,7 +30,7 @@ Furthermore, ABACUS also provides a [list of keywords](./input_files/input-main.
 To employ CMD calculations, `esolver_type` should be set to be `lj` or `dp`.
 If DP model is selected, the filename of DP model is specified by keyword `pot_file`.
 
-The MD output information will be written into the file `MD_dump`， in which the atomic forces, atomic velocities, and lattice virial are controlled by keyword `out_force`, `out_vel`, and `out_virial`, respectively.
+The MD output information will be written into the file `MD_dump`， in which the atomic forces, atomic velocities, and lattice virial are controlled by keyword `dump_force`, `dump_vel`, and `dump_virial`, respectively.
 
 [Examples](https://github.com/deepmodeling/abacus-develop/tree/develop/examples/md/lcao_gammaonly_Sn64) of MD simulations are also provided.
 There are eight INPUT files corresponding to eight different MD evolution methods in the directory.
diff --git a/source/module_io/input.cpp b/source/module_io/input.cpp
@@ -186,9 +186,9 @@ void Input::Default(void)
     init_vel = false;
     symmetry_prec = 1.0e-5; // LiuXh add 2021-08-12, accuracy for symmetry
     cal_force = 0;
-    out_force = false;
-    out_vel = false;
-    out_virial = false;
+    dump_force = true;
+    dump_vel = true;
+    dump_virial = true;
     force_thr = 1.0e-3;
     force_thr_ev2 = 0;
     stress_thr = 1.0e-2; // LiuXh add 20180515
@@ -844,17 +844,17 @@ bool Input::Read(const std::string &fn)
         {
             read_bool(ifs, cal_force);
         }
-        else if (strcmp("out_force", word) == 0)
+        else if (strcmp("dump_force", word) == 0)
         {
-            read_bool(ifs, out_force);
+            read_bool(ifs, dump_force);
         }
-        else if (strcmp("out_vel", word) == 0)
+        else if (strcmp("dump_vel", word) == 0)
         {
-            read_bool(ifs, out_vel);
+            read_bool(ifs, dump_vel);
         }
-        else if (strcmp("out_virial", word) == 0)
+        else if (strcmp("dump_virial", word) == 0)
         {
-            read_bool(ifs, out_virial);
+            read_bool(ifs, dump_virial);
         }
         else if (strcmp("force_thr", word) == 0)
         {
@@ -2709,9 +2709,9 @@ void Input::Bcast()
     Parallel_Common::bcast_bool(init_vel); // liuyu 2021-07-14
     Parallel_Common::bcast_double(symmetry_prec); // LiuXh add 2021-08-12, accuracy for symmetry
     Parallel_Common::bcast_bool(cal_force);
-    Parallel_Common::bcast_bool(out_force);
-    Parallel_Common::bcast_bool(out_vel);
-    Parallel_Common::bcast_bool(out_virial);
+    Parallel_Common::bcast_bool(dump_force);
+    Parallel_Common::bcast_bool(dump_vel);
+    Parallel_Common::bcast_bool(dump_virial);
     Parallel_Common::bcast_double(force_thr);
     Parallel_Common::bcast_double(force_thr_ev2);
     Parallel_Common::bcast_double(stress_thr); // LiuXh add 20180515
diff --git a/source/module_io/input.h b/source/module_io/input.h
@@ -46,7 +46,7 @@ class Input
     int pw_seed; // random seed for initializing wave functions qianrui 2021-8-12
 
     bool init_vel; // read velocity from STRU or not  liuyu 2021-07-14
-    bool out_vel;    // output atomic velocities into the file MD_dump or not. liuyu 2023-03-01
+    bool dump_vel;    // output atomic velocities into the file MD_dump or not. liuyu 2023-03-01
 
     /* symmetry level: 
       -1, no symmetry at all; 
@@ -107,7 +107,7 @@ class Input
     // Forces
     //==========================================================
     bool cal_force;
-    bool out_force;    // output atomic forces into the file MD_dump or not. liuyu 2023-03-01
+    bool dump_force;    // output atomic forces into the file MD_dump or not. liuyu 2023-03-01
     double force_thr; // threshold of force in unit (Ry/Bohr)
     double force_thr_ev2; // invalid force threshold, mohan add 2011-04-17
 
@@ -119,7 +119,7 @@ class Input
     double press2;
     double press3;
     bool cal_stress; // calculate the stress
-    bool out_virial;    // output lattice virial into the file MD_dump or not. liuyu 2023-03-01
+    bool dump_virial;    // output lattice virial into the file MD_dump or not. liuyu 2023-03-01
 
     std::string fixed_axes; // which axes are fixed
     bool fixed_ibrav; //whether to keep type of lattice; must be used along with latname
diff --git a/source/module_io/test/INPUT b/source/module_io/test/INPUT
@@ -85,7 +85,6 @@ cond_nonlocal                  1 #Nonlocal effects for conductivities
 #Parameters (4.Relaxation)
 ks_solver                      genelpa #cg; dav; lapack; genelpa; scalapack_gvx; cusolver
 scf_nmax                       50 ##number of electron iterations
-out_force                      0 #output the out_force or not
 relax_nmax                     1 #number of ion iteration steps
 out_stru                       0 #output the structure files after each ion step
 force_thr                      0.001 #force threshold, unit: Ry/Bohr
@@ -198,6 +197,9 @@ md_pchain                      1 #num of thermostats coupled with barostat
 md_pfirst                      -1 #initial target pressure
 md_plast                       -1 #final target pressure
 md_pfreq                       0 #oscillation frequency, used to determine qmass of thermostats coupled with barostat
+dump_force                     0 #output atomic forces into the file MD_dump or not.
+dump_vel                       0 #output atomic velocities into the file MD_dump or not
+dump_virial                    0 #output lattice virial into the file MD_dump or not
 
 #Parameters (10.Electric field and dipole correction)
 efield_flag                    0 #add electric field
diff --git a/source/module_io/test/input_test.cpp b/source/module_io/test/input_test.cpp
@@ -80,7 +80,9 @@ TEST_F(InputTest, Default)
         EXPECT_FALSE(INPUT.init_vel);
         EXPECT_DOUBLE_EQ(INPUT.symmetry_prec,1.0e-5);
         EXPECT_EQ(INPUT.cal_force,0);
-        EXPECT_FALSE(INPUT.out_force);
+        EXPECT_TRUE(INPUT.dump_force);
+        EXPECT_TRUE(INPUT.dump_vel);
+        EXPECT_TRUE(INPUT.dump_virial);
         EXPECT_DOUBLE_EQ(INPUT.force_thr,1.0e-3);
         EXPECT_DOUBLE_EQ(INPUT.force_thr_ev2,0);
         EXPECT_DOUBLE_EQ(INPUT.stress_thr,1.0e-2);
@@ -404,7 +406,9 @@ TEST_F(InputTest, Read)
         EXPECT_FALSE(INPUT.init_vel);
         EXPECT_DOUBLE_EQ(INPUT.symmetry_prec,1.0e-5);
         EXPECT_EQ(INPUT.cal_force,0);
-        EXPECT_FALSE(INPUT.out_force);
+        EXPECT_FALSE(INPUT.dump_force);
+        EXPECT_FALSE(INPUT.dump_vel);
+        EXPECT_FALSE(INPUT.dump_virial);
         EXPECT_NEAR(INPUT.force_thr,1.0e-3,1.0e-7);
         EXPECT_DOUBLE_EQ(INPUT.force_thr_ev2,0);
         EXPECT_DOUBLE_EQ(INPUT.stress_thr,1.0e-2);
diff --git a/source/module_io/write_input.cpp b/source/module_io/write_input.cpp
@@ -267,9 +267,9 @@ ModuleBase::GlobalFunc::OUTP(ofs, "out_bandgap", out_bandgap, "if true, print ou
     ModuleBase::GlobalFunc::OUTP(ofs,"md_pfirst",mdp.md_pfirst,"initial target pressure");
     ModuleBase::GlobalFunc::OUTP(ofs,"md_plast",mdp.md_plast,"final target pressure");
     ModuleBase::GlobalFunc::OUTP(ofs,"md_pfreq",mdp.md_pfreq,"oscillation frequency, used to determine qmass of thermostats coupled with barostat");
-    ModuleBase::GlobalFunc::OUTP(ofs, "out_force", out_force, "output atomic forces into the file MD_dump or not");
-    ModuleBase::GlobalFunc::OUTP(ofs, "out_vel", out_vel, "output atomic velocities into the file MD_dump or not");
-    ModuleBase::GlobalFunc::OUTP(ofs, "out_virial", out_virial, "output atomic velocities into the file MD_dump or not");
+    ModuleBase::GlobalFunc::OUTP(ofs, "dump_force", dump_force, "output atomic forces into the file MD_dump or not");
+    ModuleBase::GlobalFunc::OUTP(ofs, "dump_vel", dump_vel, "output atomic velocities into the file MD_dump or not");
+    ModuleBase::GlobalFunc::OUTP(ofs, "dump_virial", dump_virial, "output lattice virial into the file MD_dump or not");
 
     ofs << "\n#Parameters (10.Electric field and dipole correction)" << std::endl;
     ModuleBase::GlobalFunc::OUTP(ofs,"efield_flag",efield_flag,"add electric field");
diff --git a/source/module_md/MD_func.cpp b/source/module_md/MD_func.cpp
@@ -300,7 +300,7 @@ void MD_func::MDdump(const int &step,
     ofs << "  " << unit_in.latvec.e21 << "  " << unit_in.latvec.e22 << "  " << unit_in.latvec.e23 << std::endl;
     ofs << "  " << unit_in.latvec.e31 << "  " << unit_in.latvec.e32 << "  " << unit_in.latvec.e33 << std::endl;
 
-    if(GlobalV::CAL_STRESS && inp.out_virial)
+    if(GlobalV::CAL_STRESS && inp.dump_virial)
     {
         ofs << "VIRIAL (kBar)" << std::endl;
         for(int i=0; i<3; ++i)
@@ -312,11 +312,11 @@ void MD_func::MDdump(const int &step,
     }
 
     ofs << "INDEX    LABEL    POSITION (Angstrom)";
-    if(inp.out_force)
+    if(inp.dump_force)
     {
         ofs << "    FORCE (eV/Angstrom)";
     }
-    if(inp.out_vel)
+    if(inp.dump_vel)
     {
         ofs << "    VELOCITY (Angstrom/fs)";
     }
@@ -333,14 +333,14 @@ void MD_func::MDdump(const int &step,
             << "  " << unit_in.atoms[it].tau[ia].y * unit_pos
             << "  " << unit_in.atoms[it].tau[ia].z * unit_pos;
 
-            if(inp.out_force)
+            if(inp.dump_force)
             {
                 ofs << "  " << force[index].x * unit_force
                     << "  " << force[index].y * unit_force
                     << "  " << force[index].z * unit_force;
             }
 
-            if(inp.out_vel)
+            if(inp.dump_vel)
             {
                 ofs << "  " << vel[index].x * unit_vel
                     << "  " << vel[index].y * unit_vel
diff --git a/source/module_md/test/setcell.h b/source/module_md/test/setcell.h
@@ -111,9 +111,9 @@ class Setcell
         GlobalV::SEARCH_RADIUS = 8.5 * ModuleBase::ANGSTROM_AU;
         GlobalV::CAL_STRESS = 1;
 
-        INPUT.out_virial = true;
-        INPUT.out_force = true;
-        INPUT.out_vel = true;
+        INPUT.dump_virial = true;
+        INPUT.dump_force = true;
+        INPUT.dump_vel = true;
 
         INPUT.mdp.md_restart = 0;
         INPUT.mdp.md_dt = 1;

Original file line number	Diff line number	Diff line change
`@@ -186,9 +186,9 @@ void Input::Default(void)`
`186`	`186`	`init_vel = false;`
`187`	`187`	`symmetry_prec = 1.0e-5; // LiuXh add 2021-08-12, accuracy for symmetry`
`188`	`188`	`cal_force = 0;`
`189`		`- out_force = false;`
`190`		`- out_vel = false;`
`191`		`- out_virial = false;`
	`189`	`+ dump_force = true;`
	`190`	`+ dump_vel = true;`
	`191`	`+ dump_virial = true;`
`192`	`192`	`force_thr = 1.0e-3;`
`193`	`193`	`force_thr_ev2 = 0;`
`194`	`194`	`stress_thr = 1.0e-2; // LiuXh add 20180515`
`@@ -844,17 +844,17 @@ bool Input::Read(const std::string &fn)`
`844`	`844`	`{`
`845`	`845`	`read_bool(ifs, cal_force);`
`846`	`846`	`}`
`847`		`- else if (strcmp("out_force", word) == 0)`
	`847`	`+ else if (strcmp("dump_force", word) == 0)`
`848`	`848`	`{`
`849`		`- read_bool(ifs, out_force);`
	`849`	`+ read_bool(ifs, dump_force);`
`850`	`850`	`}`
`851`		`- else if (strcmp("out_vel", word) == 0)`
	`851`	`+ else if (strcmp("dump_vel", word) == 0)`
`852`	`852`	`{`
`853`		`- read_bool(ifs, out_vel);`
	`853`	`+ read_bool(ifs, dump_vel);`
`854`	`854`	`}`
`855`		`- else if (strcmp("out_virial", word) == 0)`
	`855`	`+ else if (strcmp("dump_virial", word) == 0)`
`856`	`856`	`{`
`857`		`- read_bool(ifs, out_virial);`
	`857`	`+ read_bool(ifs, dump_virial);`
`858`	`858`	`}`
`859`	`859`	`else if (strcmp("force_thr", word) == 0)`
`860`	`860`	`{`
`@@ -2709,9 +2709,9 @@ void Input::Bcast()`
`2709`	`2709`	`Parallel_Common::bcast_bool(init_vel); // liuyu 2021-07-14`
`2710`	`2710`	`Parallel_Common::bcast_double(symmetry_prec); // LiuXh add 2021-08-12, accuracy for symmetry`
`2711`	`2711`	`Parallel_Common::bcast_bool(cal_force);`
`2712`		`- Parallel_Common::bcast_bool(out_force);`
`2713`		`- Parallel_Common::bcast_bool(out_vel);`
`2714`		`- Parallel_Common::bcast_bool(out_virial);`
	`2712`	`+ Parallel_Common::bcast_bool(dump_force);`
	`2713`	`+ Parallel_Common::bcast_bool(dump_vel);`
	`2714`	`+ Parallel_Common::bcast_bool(dump_virial);`
`2715`	`2715`	`Parallel_Common::bcast_double(force_thr);`
`2716`	`2716`	`Parallel_Common::bcast_double(force_thr_ev2);`
`2717`	`2717`	`Parallel_Common::bcast_double(stress_thr); // LiuXh add 20180515`
Original file line number	Diff line number	Diff line change
`@@ -300,7 +300,7 @@ void MD_func::MDdump(const int &step,`
`300`	`300`	`ofs << " " << unit_in.latvec.e21 << " " << unit_in.latvec.e22 << " " << unit_in.latvec.e23 << std::endl;`
`301`	`301`	`ofs << " " << unit_in.latvec.e31 << " " << unit_in.latvec.e32 << " " << unit_in.latvec.e33 << std::endl;`
`302`	`302`
`303`		`- if(GlobalV::CAL_STRESS && inp.out_virial)`
	`303`	`+ if(GlobalV::CAL_STRESS && inp.dump_virial)`
`304`	`304`	`{`
`305`	`305`	`ofs << "VIRIAL (kBar)" << std::endl;`
`306`	`306`	`for(int i=0; i<3; ++i)`
`@@ -312,11 +312,11 @@ void MD_func::MDdump(const int &step,`
`312`	`312`	`}`
`313`	`313`
`314`	`314`	`ofs << "INDEX LABEL POSITION (Angstrom)";`
`315`		`- if(inp.out_force)`
	`315`	`+ if(inp.dump_force)`
`316`	`316`	`{`
`317`	`317`	`ofs << " FORCE (eV/Angstrom)";`
`318`	`318`	`}`
`319`		`- if(inp.out_vel)`
	`319`	`+ if(inp.dump_vel)`
`320`	`320`	`{`
`321`	`321`	`ofs << " VELOCITY (Angstrom/fs)";`
`322`	`322`	`}`
`@@ -333,14 +333,14 @@ void MD_func::MDdump(const int &step,`
`333`	`333`	`<< " " << unit_in.atoms[it].tau[ia].y * unit_pos`
`334`	`334`	`<< " " << unit_in.atoms[it].tau[ia].z * unit_pos;`
`335`	`335`
`336`		`- if(inp.out_force)`
	`336`	`+ if(inp.dump_force)`
`337`	`337`	`{`
`338`	`338`	`ofs << " " << force[index].x * unit_force`
`339`	`339`	`<< " " << force[index].y * unit_force`
`340`	`340`	`<< " " << force[index].z * unit_force;`
`341`	`341`	`}`
`342`	`342`
`343`		`- if(inp.out_vel)`
	`343`	`+ if(inp.dump_vel)`
`344`	`344`	`{`
`345`	`345`	`ofs << " " << vel[index].x * unit_vel`
`346`	`346`	`<< " " << vel[index].y * unit_vel`