Merge branch 'develop' of https://github.com/deepmodeling/abacus-develop into develop

YuLiu98 · YuLiu98 · commit 7dd491059a18 · 2022-05-31T16:03:32.000+08:00
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -53,6 +53,8 @@ target_link_libraries(${ABACUS_BIN_NAME} Threads::Threads)
 if(USE_OPENMP)
   find_package(OpenMP REQUIRED)
   target_link_libraries(${ABACUS_BIN_NAME} OpenMP::OpenMP_CXX)
+  add_compile_options(${OpenMP_CXX_FLAGS})
+  add_link_options(${OpenMP_CXX_LIBRARIES})
 endif()
 
 include(CheckLanguage)
diff --git a/source/module_md/FIRE.cpp b/source/module_md/FIRE.cpp
@@ -64,6 +64,7 @@ void FIRE::first_half()
     }
 #ifdef __MPI
     MPI_Bcast(pos , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    MPI_Bcast(vel , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);
 #endif
 
     ucell.update_pos_tau(pos);
diff --git a/source/module_md/MD_func.cpp b/source/module_md/MD_func.cpp
@@ -75,38 +75,35 @@ void MD_func::kinetic_stress(
 //   This function calculates the classical kinetic energy of atoms
 //   and its contribution to stress.
 //----------------------------------------------------------------------------
-    if(GlobalV::MY_RANK==0) //only first rank do md
+    kinetic = MD_func::GetAtomKE(unit_in.nat, vel, allmass);
+
+    if(GlobalV::CAL_STRESS)
     {
-        kinetic = MD_func::GetAtomKE(unit_in.nat, vel, allmass);
+        ModuleBase::matrix temp;
+        temp.create(3,3);    // initialize
 
-        if(GlobalV::CAL_STRESS)
+        for(int ion=0; ion<unit_in.nat; ++ion)
         {
-            ModuleBase::matrix temp;
-            temp.create(3,3);    // initialize
-
-            for(int ion=0; ion<unit_in.nat; ++ion)
+            for(int i=0; i<3; ++i)
             {
-                for(int i=0; i<3; ++i)
+                for(int j=i; j<3; ++j)
                 {
-                    for(int j=i; j<3; ++j)
-                    {
-                        temp(i, j) += allmass[ion] * vel[ion][i] * vel[ion][j];
-                    }
+                    temp(i, j) += allmass[ion] * vel[ion][i] * vel[ion][j];
                 }
             }
+        }
 
-            for(int i=0; i<3; ++i)
+        for(int i=0; i<3; ++i)
+        {
+            for(int j=0; j<3; ++j)
             {
-                for(int j=0; j<3; ++j)
+                if(j<i) 
+                {
+                    stress(i, j) = stress(j, i);
+                }
+                else
                 {
-                    if(j<i) 
-                    {
-                        stress(i, j) = stress(j, i);
-                    }
-                    else
-                    {
-                        stress(i, j) = temp(i, j)/unit_in.omega;
-                    }
+                    stress(i, j) = temp(i, j)/unit_in.omega;
                 }
             }
         }
diff --git a/source/module_md/MSST.cpp b/source/module_md/MSST.cpp
@@ -79,8 +79,6 @@ void MSST::first_half()
     const int sd = mdp.msst_direction;
     const double dthalf = 0.5 * mdp.md_dt;
     double vol;
-    if( GlobalV::MY_RANK == 0 )
-    {
     energy_ = potential + kinetic;
 
     // propagate the time derivative of volume 1/2 step
@@ -119,9 +117,9 @@ void MSST::first_half()
     {
         pos[i] += vel[i] * mdp.md_dt;
     }
-    }
 #ifdef __MPI
     MPI_Bcast(pos , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    MPI_Bcast(vel , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);
 #endif
 
     ucell.update_pos_tau(pos);
@@ -143,8 +141,6 @@ void MSST::second_half()
 
     const int sd = mdp.msst_direction;
     const double dthalf = 0.5 * mdp.md_dt;
-    if( GlobalV::MY_RANK == 0 )
-    {
     energy_ = potential + kinetic;
 
     // propagate velocities 1/2 step
@@ -159,7 +155,6 @@ void MSST::second_half()
 
     // calculate Lagrangian position
     lag_pos -= mdp.msst_vel * ucell.omega / v0 * mdp.md_dt;
-    }
 
     ModuleBase::timer::tick("MSST", "second_half");
 }
diff --git a/source/module_md/verlet.cpp b/source/module_md/verlet.cpp
@@ -89,6 +89,7 @@ void Verlet::first_half()
     }
 #ifdef __MPI
     MPI_Bcast(pos , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    MPI_Bcast(vel , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);
 #endif
 
     ucell.update_pos_tau(pos);
@@ -98,7 +99,6 @@ void Verlet::first_half()
 
 void Verlet::second_half()
 {
-    if(GlobalV::MY_RANK==0) //only first rank do md
     for(int i=0; i<ucell.nat; ++i)
     {
         for(int k=0; k<3; ++k)
diff --git a/tests/integrate/107_PW_outWfcR/INPUT b/tests/integrate/107_PW_outWfcR/INPUT
@@ -0,0 +1,19 @@
+INPUT_PARAMETERS
+#Parameters (1.General)
+suffix			autotest
+calculation     scf
+ntype			1
+nbands			6
+symmetry		1
+pseudo_dir      ../tools/PP_ORB/
+pseudo_type     upf201
+
+#Parameters (2.Iteration)
+ecutwfc			20
+scf_thr				1e-9
+scf_nmax			100
+
+#Parameters (3.Basis)
+basis_type		pw
+
+out_wfc_r 1
diff --git a/tests/integrate/107_PW_outWfcR/KPT b/tests/integrate/107_PW_outWfcR/KPT
@@ -0,0 +1,4 @@
+K_POINTS
+0
+Gamma
+1 1 1 0 0 0
diff --git a/tests/integrate/107_PW_outWfcR/STRU b/tests/integrate/107_PW_outWfcR/STRU
@@ -0,0 +1,19 @@
+ATOMIC_SPECIES
+Si 14 Si_ONCV_PBE-1.0.upf
+
+LATTICE_CONSTANT
+10.2  // add lattice constant
+
+LATTICE_VECTORS
+0.5 0.5 0.0
+0.5 0.0 0.5
+0.0 0.5 0.5
+
+ATOMIC_POSITIONS
+Direct 
+
+Si	// Element type	
+0.0	// magnetism
+2	
+0.00 0.00 0.00 1 1 1
+0.25 0.25 0.25 1 1 1
diff --git a/tests/integrate/107_PW_outWfcR/jd b/tests/integrate/107_PW_outWfcR/jd
@@ -0,0 +1 @@
+test the output of wfc_r, and compare the variance
diff --git a/tests/integrate/107_PW_outWfcR/result.ref b/tests/integrate/107_PW_outWfcR/result.ref
@@ -0,0 +1,9 @@
+etotref -197.1405644352783
+etotperatomref -98.5702822176
+variance_wfc_r_0_0 0.31340
+variance_wfc_r_0_1 2.68637
+variance_wfc_r_0_2 1.89907
+variance_wfc_r_0_3 1.96089
+variance_wfc_r_0_4 1.26491
+variance_wfc_r_0_5 0.84051
+totaltimeref 0.20294
diff --git a/tests/integrate/312_NO_GO_wfc_istate/INPUT b/tests/integrate/312_NO_GO_wfc_istate/INPUT
@@ -0,0 +1,19 @@
+INPUT_PARAMETERS
+#Parameters	(System)
+suffix                  autotest
+ntype			1
+nbands			4
+stru_file		STRU
+kpoint_file		KPT
+pseudo_dir		../tools/PP_ORB/
+orbital_dir		../tools/PP_ORB/
+latname			sc
+#Parameters (PW)
+ecutwfc			25.0              # Rydberg
+#Parameters (electronic)
+basis_type		lcao 	
+scf_thr			1e-10
+
+calculation     	istate
+gamma_only		1
+read_file_dir 		./
diff --git a/tests/integrate/312_NO_GO_wfc_istate/KPT b/tests/integrate/312_NO_GO_wfc_istate/KPT
@@ -0,0 +1,4 @@
+K_POINTS
+0
+Gamma
+1 1 1 0 0 0
diff --git a/tests/integrate/312_NO_GO_wfc_istate/LOWF_GAMMA_S1.dat b/tests/integrate/312_NO_GO_wfc_istate/LOWF_GAMMA_S1.dat
@@ -0,0 +1,22 @@
+4 (number of bands)
+10 (number of orbitals)
+1 (band)
+-7.57096415e-01 (Ry)
+2.00000000e+00 (Occupations)
+-5.37362289e-01 -3.68451648e-02 -1.55131570e-02 -2.64865890e-16 1.05515886e-16 
+-5.37362289e-01 -3.68451648e-02 1.55131570e-02 2.31512618e-16 -9.17998044e-17 
+2 (band)
+3.05607270e-01 (Ry)
+0.00000000e+00 (Occupations)
+1.86655079e+00 -5.99493369e-01 6.23278504e-02 -6.10257790e-16 -1.07130366e-15 
+-1.86655079e+00 5.99493369e-01 6.23278504e-02 -9.70034830e-16 3.67511274e-16 
+3 (band)
+7.03394915e-01 (Ry)
+0.00000000e+00 (Occupations)
+3.77198799e-02 5.60791988e-01 2.09803877e-02 4.76540590e-17 -1.21321449e-16 
+3.77198799e-02 5.60791988e-01 -2.09803877e-02 -8.28199028e-16 8.17735629e-17 
+4 (band)
+1.63463390e+00 (Ry)
+0.00000000e+00 (Occupations)
+1.12080703e+00 -7.94507151e-01 6.75140264e-01 -8.64606026e-16 -1.08079951e-15 
+-1.12080703e+00 7.94507151e-01 6.75140264e-01 -2.39467947e-15 1.47720374e-16 
diff --git a/tests/integrate/312_NO_GO_wfc_istate/STRU b/tests/integrate/312_NO_GO_wfc_istate/STRU
@@ -0,0 +1,19 @@
+#This is the atom file containing all the information
+#about the lattice structure.
+
+ATOMIC_SPECIES
+H 1.0008  H_ONCV_PBE-1.0.upf 
+ 
+NUMERICAL_ORBITAL
+H_gga_6au_60Ry_2s1p.orb
+
+LATTICE_CONSTANT
+10.0  			#Lattice constant
+
+ATOMIC_POSITIONS
+Cartesian   		#Cartesian(Unit is LATTICE_CONSTANT)
+H 			#Name of element	
+0.0			#Magnetic for this element.
+2			#Number of atoms
+0.00 0.00 -0.0661400 0 0 0	#x,y,z, move_x, move_y, move_z
+0.00 0.00  0.0661400 0 0 0	#x,y,z, move_x, move_y, move_z
diff --git a/tests/integrate/312_NO_GO_wfc_istate/jd b/tests/integrate/312_NO_GO_wfc_istate/jd
@@ -0,0 +1 @@
+istate calculation for lcao gamma_only
diff --git a/tests/integrate/312_NO_GO_wfc_istate/result.ref b/tests/integrate/312_NO_GO_wfc_istate/result.ref
@@ -0,0 +1,9 @@
+BAND1_CHG 2.00064
+BAND2_CHG 2.00508
+BAND3_CHG 2.0031
+BAND4_CHG 2.01085
+BAND1_SPIN0_CHG.cube 2.06078
+BAND2_SPIN0_CHG.cube 2.07625
+BAND3_SPIN0_CHG.cube 2.07026
+BAND4_SPIN0_CHG.cube 2.0698
+totaltimeref 0.39732
diff --git a/tests/integrate/CASES b/tests/integrate/CASES
@@ -29,6 +29,7 @@
 106_PW_PU_chargemixing
 107_PW_OB_outputbands
 107_PW_OD_outputdos
+107_PW_outWfcR
 108_PW_RE
 108_PW_RE_MB
 108_PW_RE_MG
@@ -133,6 +134,7 @@
 311_NO_GO_S2_elec_minus
 312_NO_GO_wfc_out
 312_NO_GO_wfc_ienvelope
+312_NO_GO_wfc_istate
 320_NO_GO_MD_FIRE
 320_NO_GO_MD_NVE
 320_NO_GO_MD_NVT
diff --git a/tests/integrate/CMakeLists.txt b/tests/integrate/CMakeLists.txt
@@ -14,4 +14,8 @@ else()
     )
     add_executable(sum_ENV_H2 ${ABACUS_TEST_DIR}/integrate/tools/sum_ENV_H2.cpp)
     install(TARGETS sum_ENV_H2 DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
+    add_executable(sum_BAND_CHG_H2 ${ABACUS_TEST_DIR}/integrate/tools/sum_BAND_CHG_H2.cpp)
+    install(TARGETS sum_BAND_CHG_H2 DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
+    add_executable(sum_BAND_CHG_H2_cube ${ABACUS_TEST_DIR}/integrate/tools/sum_BAND_CHG_H2_cube.cpp)
+    install(TARGETS sum_BAND_CHG_H2_cube DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
 endif()
diff --git a/tests/integrate/tools/catch_properties.sh b/tests/integrate/tools/catch_properties.sh
@@ -36,6 +36,7 @@ has_r=`grep -En '(^|[[:space:]])out_mat_r($|[[:space:]])' INPUT | awk '{print $2
 deepks_out_labels=`grep deepks_out_labels INPUT | awk '{print $2}' | sed s/[[:space:]]//g`
 deepks_bandgap=`grep deepks_bandgap INPUT | awk '{print $2}' | sed s/[[:space:]]//g`
 has_lowf=`grep out_wfc_lcao INPUT | awk '{print $2}' | sed s/[[:space:]]//g`
+has_wfc_r=`grep out_wfc_r INPUT | awk '{print $2}' | sed s/[[:space:]]//g`
 gamma_only=`grep gamma_only INPUT | awk '{print $2}' | sed s/[[:space:]]//g`
 #echo $running_path
 base=`grep -En '(^|[[:space:]])basis_type($|[[:space:]])' INPUT | awk '{print $2}' | sed s/[[:space:]]//g`
@@ -48,7 +49,8 @@ test -e $1 && rm $1
 #--------------------------------------------
 # if NOT non-self-consistent calculations
 #--------------------------------------------
-if [ $calculation != "nscf" ] && [ $calculation != "ienvelope" ]; then
+if [ $calculation != "nscf" ] && [ $calculation != "ienvelope" ]\
+&& [ $calculation != "istate" ]	; then
 	etot=`grep ETOT_ $running_path | awk '{print $2}'`
 	etotperatom=`awk 'BEGIN {x='$etot';y='$natom';printf "%.10f\n",x/y}'`
 	echo "etotref $etot" >>$1
@@ -109,6 +111,28 @@ if ! test -z "$has_hs"  && [  $has_hs -eq 1 ]; then
 	total_s=`sum_file OUT.autotest/data-0-S`
 	echo "totalSmatrix $total_s" >>$1
 fi
+
+# echo "$has_wfc_r" ## test out_wfc_r > 0
+if ! test -z "$has_wfc_r"  && [ $has_wfc_r -eq 1 ]; then
+	if [[ ! -f OUT.autotest/running_scf.log ]];then
+		echo "Can't find file OUT.autotest/running_scf.log"
+		exit 1
+	fi
+	nband=$(grep NBANDS OUT.autotest/running_scf.log|awk '{print $3}')
+	allgrid=$(grep "fft grid for wave functions" OUT.autotest/running_scf.log|awk -F "[=,]" '{print $2*$3*$4}')
+	for((band=0;band<$nband;band++));do
+		if [[ -f "OUT.autotest/wfc_realspace/wfc_realspace_0_$band" ]];then
+			variance_wfc_r=`sed -n "13,$"p OUT.autotest/wfc_realspace/wfc_realspace_0_$band | \
+						awk -v all=$allgrid 'BEGIN {sumall=0} {for(i=1;i<=NF;i++) {sumall+=($i-1)*($i-1)}}\
+						END {printf"%.5f",(sumall/all)}'`
+			echo "variance_wfc_r_0_$band $variance_wfc_r" >>$1
+		else
+			echo "Can't find file OUT.autotest/wfc_realspace/wfc_realspace_0_$band"
+			exit 1
+		fi
+	done
+fi	
+
 # echo "$has_lowf" ## test out_wfc_lcao > 0
 if ! test -z "$has_lowf"  && [ $has_lowf -eq 1 ]; then
 	if ! test -z "$gamma_only"  && [ $gamma_only -eq 1 ]; then
@@ -142,12 +166,42 @@ fi
 if [ $calculation == "ienvelope" ]; then
 	nfile=0
 	envfiles=`ls OUT.autotest/ | grep ENV`
-	for env in $envfiles; 
-	do
-		nelec=`../tools/sum_ENV_H2 OUT.autotest/$env`
-		nfile=$(($nfile+1))
-		echo "nelec$nfile $nelec" >>$1	
-	done
+	if test -z "$envfiles"; then
+		echo "Can't find ENV(-elope) files"
+		exit 1
+	else
+		for env in $envfiles;
+		do
+			nelec=`../tools/sum_ENV_H2 OUT.autotest/$env`
+			nfile=$(($nfile+1))
+			echo "nelec$nfile $nelec" >>$1	
+		done
+	fi
+fi
+
+if [ $calculation == "istate" ]; then
+	chgfiles=`ls OUT.autotest/ | grep -E '_CHG$'`
+	if test -z "$chgfiles"; then
+		echo "Can't find BAND_CHG files"
+		exit 1
+	else
+		for chg in $chgfiles;
+		do
+			total_chg=`../tools/sum_BAND_CHG_H2 OUT.autotest/$chg`
+			echo "$chg $total_chg" >>$1
+		done
+	fi
+	cubefiles=`ls OUT.autotest/ | grep -E '.cube$'`
+	if test -z "$cubefiles"; then
+		echo "Can't find BAND_CHG files"
+		exit 1
+	else
+		for cube in $cubefiles;
+		do
+			total_chg=`../tools/sum_BAND_CHG_H2_cube OUT.autotest/$cube`
+			echo "$cube $total_chg" >>$1
+		done
+	fi
 fi
 
 #echo $total_band
diff --git a/tests/integrate/tools/sum_BAND_CHG_H2.cpp b/tests/integrate/tools/sum_BAND_CHG_H2.cpp
diff --git a/tests/integrate/tools/sum_BAND_CHG_H2_cube.cpp b/tests/integrate/tools/sum_BAND_CHG_H2_cube.cpp

Original file line number	Diff line number	Diff line change
`@@ -64,6 +64,7 @@ void FIRE::first_half()`
`64`	`64`	`}`
`65`	`65`	`#ifdef __MPI`
`66`	`66`	`MPI_Bcast(pos , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);`
	`67`	`+ MPI_Bcast(vel , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);`
`67`	`68`	`#endif`
`68`	`69`
`69`	`70`	`ucell.update_pos_tau(pos);`
Original file line number	Diff line number	Diff line change
`@@ -75,38 +75,35 @@ void MD_func::kinetic_stress(`
`75`	`75`	`// This function calculates the classical kinetic energy of atoms`
`76`	`76`	`// and its contribution to stress.`
`77`	`77`	`//----------------------------------------------------------------------------`
`78`		`- if(GlobalV::MY_RANK==0) //only first rank do md`
	`78`	`+ kinetic = MD_func::GetAtomKE(unit_in.nat, vel, allmass);`
	`79`	`+`
	`80`	`+ if(GlobalV::CAL_STRESS)`
`79`	`81`	`{`
`80`		`- kinetic = MD_func::GetAtomKE(unit_in.nat, vel, allmass);`
	`82`	`+ ModuleBase::matrix temp;`
	`83`	`+ temp.create(3,3); // initialize`
`81`	`84`
`82`		`- if(GlobalV::CAL_STRESS)`
	`85`	`+ for(int ion=0; ion<unit_in.nat; ++ion)`
`83`	`86`	`{`
`84`		`- ModuleBase::matrix temp;`
`85`		`- temp.create(3,3); // initialize`
`86`		`-`
`87`		`- for(int ion=0; ion<unit_in.nat; ++ion)`
	`87`	`+ for(int i=0; i<3; ++i)`
`88`	`88`	`{`
`89`		`- for(int i=0; i<3; ++i)`
	`89`	`+ for(int j=i; j<3; ++j)`
`90`	`90`	`{`
`91`		`- for(int j=i; j<3; ++j)`
`92`		`- {`
`93`		`- temp(i, j) += allmass[ion] * vel[ion][i] * vel[ion][j];`
`94`		`- }`
	`91`	`+ temp(i, j) += allmass[ion] * vel[ion][i] * vel[ion][j];`
`95`	`92`	`}`
`96`	`93`	`}`
	`94`	`+ }`
`97`	`95`
`98`		`- for(int i=0; i<3; ++i)`
	`96`	`+ for(int i=0; i<3; ++i)`
	`97`	`+ {`
	`98`	`+ for(int j=0; j<3; ++j)`
`99`	`99`	`{`
`100`		`- for(int j=0; j<3; ++j)`
	`100`	`+ if(j<i)`
	`101`	`+ {`
	`102`	`+ stress(i, j) = stress(j, i);`
	`103`	`+ }`
	`104`	`+ else`
`101`	`105`	`{`
`102`		`- if(j<i)`
`103`		`- {`
`104`		`- stress(i, j) = stress(j, i);`
`105`		`- }`
`106`		`- else`
`107`		`- {`
`108`		`- stress(i, j) = temp(i, j)/unit_in.omega;`
`109`		`- }`
	`106`	`+ stress(i, j) = temp(i, j)/unit_in.omega;`
`110`	`107`	`}`
`111`	`108`	`}`
`112`	`109`	`}`
Original file line number	Diff line number	Diff line change
`@@ -89,6 +89,7 @@ void Verlet::first_half()`
`89`	`89`	`}`
`90`	`90`	`#ifdef __MPI`
`91`	`91`	`MPI_Bcast(pos , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);`
	`92`	`+ MPI_Bcast(vel , ucell.nat*3,MPI_DOUBLE,0,MPI_COMM_WORLD);`
`92`	`93`	`#endif`
`93`	`94`
`94`	`95`	`ucell.update_pos_tau(pos);`
`@@ -98,7 +99,6 @@ void Verlet::first_half()`
`98`	`99`
`99`	`100`	`void Verlet::second_half()`
`100`	`101`	`{`
`101`		`- if(GlobalV::MY_RANK==0) //only first rank do md`
`102`	`102`	`for(int i=0; i<ucell.nat; ++i)`
`103`	`103`	`{`
`104`	`104`	`for(int k=0; k<3; ++k)`
-Original file line number
+Diff line change
@@ @@ -0,0 +1,4 @@ @@
 +K_POINTS
 +0
 +Gamma
 +1 1 1 0 0 0
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+test the output of wfc_r, and compare the variance`