Commit JT 021318

doc/src/fix_langevin_spin.txt

@@ -16,13 +16,12 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l
 langevin/spin = style name of this fix command :l
 T = desired temperature of the bath (temperature units, K in metal units) :l
 Tdamp = transverse magnetic damping parameter (adim) :l
-Ldamp = longitudinal magnetic damping parameter (adim) :l
 seed = random number seed to use for white noise (positive integer) :l
 :ule
 
 [Examples:]
 
-fix 2 all langevin/spin 300.0 0.01 0.0 21 :pre
+fix 2 all langevin/spin 300.0 0.01 21 :pre
 
 [Description:]
 
@@ -36,6 +35,8 @@ the following stochastic differential equation:
 :c,image(Eqs/fix_langevin_spin_sLLG.jpg)
 
 with lambda the transverse damping, and eta a random verctor.
+This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG) 
+equation.
 
 The components of eta are drawn from a Gaussian probability law. Their amplitude 
 is defined as a proportion of the temperature of the external thermostat T (in K 
@@ -43,6 +44,16 @@ in metal units).
 
 More details about this implementation are reported in "(Tranchida)"_#Tranchida1.
 
+Note: due to the form of the sLLG equation, this fix has to be the last defined 
+magnetic fix before the integration/spin fix. As an example:
+
+fix 1 all force/spin zeeman 0.01 0.0 0.0 1.0
+fix 2 all langevin/spin 300.0 0.01 21 
+fix 3 all integration/spin lattice yes :pre
+
+is correct, but defining a force/spin command after the langevin/spin command
+would send an error message. 
+
 Note: The random # {seed} must be a positive integer.  A Marsaglia random
 number generator is used.  Each processor uses the input seed to
 generate its own unique seed and its own stream of random numbers.
@@ -71,6 +82,9 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
 The numerical integration has to be performed with {fix/integration/spin} 
 when {langevin/spin} is enabled. 
 
+This fix has to be the last defined magnetic fix before the integration fix 
+("fix integration spin"_fix_integration_spin.html). 
+
 [Related commands:]
 
 "fix integration spin"_fix_integration_spin.html, 

examples/SPIN/bfo/in.spin.bfo

@@ -1,55 +1,55 @@
-# sc iron atoms in bismuth oxide 
+# layer sc iron atoms (in the [001] plane) in bismuth oxide 
 
 clear 
-units metal
+units 		metal
-atom_style spin
+atom_style 	spin
 
-dimension 3
+dimension 	3
-boundary p p p 
+boundary 	p p f
 
 # check why?
-atom_modify map array 
+atom_modify 	map array 
 
-lattice sc 3.96
+lattice 	sc 3.96
-region box block 0.0 34.0 0.0 34.0 0.0 5.0
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
-create_box 1 box
+create_box 	1 box
-create_atoms 1 box
+create_atoms 	1 box
 
 # setting mass, mag. moments, and interactions for bfo
 
 mass		1 1.0
 
-set group all spin/random 11 2.50
+set 		group all spin/random 11 2.50
 
-pair_style hybrid/overlay pair/spin/exchange 6.0 pair/spin/me 4.5
+pair_style 	hybrid/overlay pair/spin/exchange 6.0 pair/spin/me 4.5
-pair_coeff * * pair/spin/exchange exchange 6.0 -0.01575 0.0 1.965
+pair_coeff 	* * pair/spin/exchange exchange 6.0 -0.01575 0.0 1.965
-pair_coeff * * pair/spin/me me 4.5 0.000109 1.0 1.0 1.0
+#pair_coeff 	* * pair/spin/me me 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * pair/spin/me me 4.5 0.00109 1.0 1.0 1.0
 
-neighbor 0.1 bin
+neighbor 	0.1 bin
-neigh_modify every 10 check yes delay 20
+neigh_modify 	every 10 check yes delay 20
 
-fix 1 all force/spin anisotropy 0.0000035 0.0 0.0 1.0
+fix 		1 all force/spin anisotropy 0.0000033 0.0 0.0 1.0
-fix 2 all langevin/spin 0.0 0.1 0.0 21
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all integration/spin lattice no
 
-fix 3 all integration/spin lattice no
+timestep	0.0002
 
-timestep	0.0001
+compute 	out_mag all compute/spin
+compute 	out_pe all pe
+compute 	out_ke all ke
+compute 	out_temp all temp
 
-compute out_mag    all compute/spin
+variable 	magz equal c_out_mag[4]
-compute out_pe     all pe
+variable 	magnorm equal c_out_mag[5]
-compute out_ke     all ke
+variable 	emag equal c_out_mag[6]
-compute out_temp   all temp
+variable 	tmag equal c_out_mag[7]
-
+variable 	mag_force equal f_1
-variable magz      equal c_out_mag[4]
-variable magnorm   equal c_out_mag[5]
-variable emag      equal c_out_mag[6]
-variable tmag      equal c_out_mag[7]
-variable mag_force equal f_1
 
 thermo_style    custom step time v_magnorm v_emag temp etotal
-thermo          10
+thermo          50
 
-#dump 1 all custom 100 dump_spin_BFO.lammpstrj type x y z spx spy spz
+dump 		1 all custom 100 dump_spin_BFO.lammpstrj type x y z spx spy spz
 
-run 10000
+run 		20000
 

examples/SPIN/cobalt/in.spin.cobalt

@@ -31,8 +31,8 @@ pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
 neighbor 0.1 bin
 neigh_modify every 10 check yes delay 20
 
-fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
+fix 1 all force/spin zeeman 0.01 0.0 0.0 1.0
-fix 2 all langevin/spin 0.0 0.1 0.0 21
+fix 2 all langevin/spin 0.0 0.0 21
 
 fix 3 all integration/spin lattice yes
 

examples/SPIN/curie_temperature/in.spin.cobalt

@@ -32,7 +32,7 @@ neighbor 0.1 bin
 neigh_modify every 10 check yes delay 20
 
 fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
-fix 2 all langevin/spin 0.0 0.1 0.0 21
+fix 2 all langevin/spin 0.0 0.1 21
 
 fix 3 all integration/spin lattice yes
 

examples/SPIN/dev/in.spin.cobalt

@@ -48,10 +48,10 @@ velocity all create 200 4928459 rot yes dist gaussian
 #Magneto-mechanic interactions for bulk fcc Cobalt
 #pair_style pair/spin/exchange 4.0
 #pair_style eam/alloy
-#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
+pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
-pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
+#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
 
-pair_coeff * * eam/alloy ../examples/SPIN/Co_PurjaPun_2012.eam.alloy Co
+pair_coeff * * eam/alloy ../examples/SPIN/dev/Co_PurjaPun_2012.eam.alloy Co
 #pair_coeff * * ../Co_PurjaPun_2012.eam.alloy Co
 
 #pair_style pair/spin/exchange 4.0
@@ -67,7 +67,7 @@ pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
 #pair_coeff * * me 2.6 0.01 1.0 1.0 1.0
 
 #type i and j | interaction type | cutoff | K1 (eV) | K2 (adim) | K3 (Ang) (for SOC)
-#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731 
+pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731 
 #pair_coeff * * pair/spin/soc/neel neel 4.0 0.0 0.864159 2.13731 
 
 #Define a skin distance, update neigh list every 
@@ -78,13 +78,13 @@ neigh_modify every 10 check yes delay 20
 
 #Magnetic field fix
 #Type | Intensity (T or eV) | Direction
-#fix 1 all force/spin zeeman 0.0 0.0 0.0 1.0
+fix 1 all force/spin zeeman 0.0 0.0 0.0 1.0
 #fix 1 all force/spin anisotropy 0.01 0.0 0.0 1.0
 
 #Fix Langevin spins (merging damping and temperature)
 #Temp | Alpha_trans | Alpha_long | Seed
 #fix 2 all langevin/spin 0.0 0.1 0.0 21
-#fix 2 all langevin/spin 0.0 0.0 0.0 21
+fix 2 all langevin/spin 0.0 0.0 21
 
 #Magnetic integration fix
 fix 3 all integration/spin lattice yes
@@ -112,14 +112,15 @@ variable tmag      equal c_out_mag[7]
 variable mag_force equal f_1
 #variable test      equal etotal-0.5*c_out_mag[6]
 
-thermo          10
+thermo          50
-thermo_style    custom step time v_magnorm v_emag temp etotal
+#thermo_style    custom step time v_magnorm v_tmag temp etotal
+thermo_style    custom step time pe ke v_emag etotal
 thermo_modify   format float %20.15g
 
 #Dump the positions and spin directions of magnetic particles (vmd format)
-dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
+#dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
 
 #Running the simulations for N timesteps
-run 10
+#run 10
-#run 1000
+run 200000
 

examples/SPIN/iron/fe_dd.dat

@@ -0,0 +1,19 @@
+            6            8
+ Optimal parameter set
+            1    4.100199340884814       F
+            2    1.565647547483517       F
+            1   0.9332056681088162       T    3.000000000000000     
+            2   -1.162558782567700       T    2.866666666666670     
+            3  -0.3502026949249225       T    2.733333333333330     
+            4   0.4287820835430028       T    2.600000000000000     
+            5    4.907925057809273       T    2.400000000000000     
+            6   -5.307049068415304       T    2.300000000000000     
+            1  -0.1960674387419232       F    4.100000000000000     
+            2   0.3687525935422963       F    3.800000000000000     
+            3   -1.505333614924853       F    3.500000000000000     
+            4    4.948907078156191       T    3.200000000000000     
+            5   -4.894613262753399       T    2.900000000000000     
+            6    3.468897724782442       T    2.600000000000000     
+            7   -1.792218099820337       T    2.400000000000000     
+            8    80.22069592246987       T    2.300000000000000     
+

examples/SPIN/iron/in.spin.iron

@@ -0,0 +1,59 @@
+# bcc iron in a 3d periodic box
+
+clear 
+units metal
+atom_style spin
+
+dimension 3
+boundary p p p
+
+# check why?
+atom_modify map array 
+
+lattice bcc 2.8665
+region box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 1 box
+create_atoms 1 box
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+
+set group all spin/random 31 2.2
+velocity all create 100 4928459 rot yes dist gaussian
+
+#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
+pair_style hybrid/overlay eam/alloy pair/spin/exchange 3.5
+pair_coeff * * eam/alloy ../examples/SPIN/iron/Fe_Mishin2006.eam.alloy Fe
+pair_coeff * * pair/spin/exchange exchange 4.0 0.025498 0.281 1.999 
+#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731 
+
+neighbor 0.1 bin
+neigh_modify every 10 check yes delay 20
+
+fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
+fix 2 all langevin/spin 0.0 0.0 21
+
+fix 3 all integration/spin lattice yes
+
+timestep	0.0001
+
+
+compute out_mag    all compute/spin
+compute out_pe     all pe
+compute out_ke     all ke
+compute out_temp   all temp
+
+variable magz      equal c_out_mag[4]
+variable magnorm   equal c_out_mag[5]
+variable emag      equal c_out_mag[6]
+variable tmag      equal c_out_mag[7]
+variable mag_force equal f_1
+
+thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo          50
+
+dump 1 all custom 50 dump_iron.lammpstrj type x y z spx spy spz
+
+run 10000
+

examples/SPIN/nickel/in.spin.nickel

@@ -0,0 +1,59 @@
+# fcc cobalt in a 3d periodic box
+
+clear 
+units metal
+atom_style spin
+
+dimension 3
+boundary p p p
+
+# check why?
+atom_modify map array 
+
+lattice fcc 3.54
+region box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 1 box
+create_atoms 1 box
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass		1 58.93
+
+set group all spin/random 31 1.72
+velocity all create 100 4928459 rot yes dist gaussian
+
+#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
+pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
+pair_coeff * * eam/alloy ../examples/SPIN/cobalt/Co_PurjaPun_2012.eam.alloy Co
+pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 
+#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731 
+
+neighbor 0.1 bin
+neigh_modify every 10 check yes delay 20
+
+fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
+fix 2 all langevin/spin 0.0 0.1 21
+
+fix 3 all integration/spin lattice yes
+
+timestep	0.0001
+
+
+compute out_mag    all compute/spin
+compute out_pe     all pe
+compute out_ke     all ke
+compute out_temp   all temp
+
+variable magz      equal c_out_mag[4]
+variable magnorm   equal c_out_mag[5]
+variable emag      equal c_out_mag[6]
+variable tmag      equal c_out_mag[7]
+variable mag_force equal f_1
+
+thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo          10
+
+#dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
+
+run 1000
+

examples/SPIN/read_restart/in.spin.read_data

@@ -52,7 +52,7 @@ fix 1 all force/spin zeeman 0.0 0.0 0.0 1.0
 
 #Fix Langevin spins (merging damping and temperature)
 #Temp | Alpha_trans | Alpha_long | Seed
-fix 2 all langevin/spin 0.0 0.0 0.0 21
+fix 2 all langevin/spin 0.0 0.0 21
 
 #Magnetic integration fix
 fix 3 all integration/spin serial

examples/SPIN/skyrmion/in.spin.skyrmion

@@ -1,55 +1,81 @@
-# fcc cobalt in a 3d box
+# initial variables
 
-clear 
+# dimensions of the box and of each layer
-units metal
+variable 	box_size equal 50.0
-atom_style spin
+variable 	ir_thick equal 4.0
+variable 	fe_thick equal 0.5
+variable 	pd_thick equal 0.5
 
-dimension 3
+variable 	fe_hi equal ${ir_thick}+${fe_thick}
-boundary p p f
+variable	pd_hi equal ${ir_thick}+${fe_thick}+${pd_thick}
+
+ 
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p f
 
 # check why?
-atom_modify map array 
+atom_modify 	map array 
 
-lattice fcc 3.54
+lattice 	fcc 3.839 orient x 1 -1 0 orient y 1 1 -2 orient z 1 1 1
-region box block 0.0 50.0 0.0 50.0 0.0 4.0
+region 		box block 	0.0 ${box_size} 	0.0 ${box_size} 	0.0         ${pd_hi}
-create_box 1 box
+region 		box_ir block 	0.0 ${box_size} 	0.0 ${box_size}		0.0         ${ir_thick}
-create_atoms 1 box
+region 		box_fe block 	0.0 ${box_size} 	0.0 ${box_size}	 	${ir_thick} ${fe_hi}
+region 		box_pd block 	0.0 ${box_size} 	0.0 ${box_size}	 	${fe_hi}    ${pd_hi}
+
+create_box 	3 box
+
+create_atoms 	1 region box_ir
+create_atoms 	2 region box_fe
+create_atoms 	3 region box_pd
+
+group 		ir_atoms region box_ir
+group 		fe_atoms region box_fe
+group 		pd_atoms region box_pd
 
 # setting mass, mag. moments, and interactions for cobalt
 
-mass		1 58.93
+mass		1 192.217	# mass of Ir atoms
+mass		2 55.845	# mass of Fe atoms
+mass		3 106.42	# mass of Pd atoms
 
-set group all spin/random 31 1.72
+set		group ir_atoms spin/random 31 0.01	# has to set a length for LAMMPS to be happy
+set		group fe_atoms spin/random 89 2.7
+set 		group pd_atoms spin/random 55 0.3
 
-#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
+#pair_style 	hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
-pair_style hybrid/overlay pair/spin/exchange 4.0 pair/spin/soc/dmi 2.6
+pair_style 	hybrid/overlay pair/spin/exchange 4.0
-pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+#pair_style 	hybrid/overlay pair/spin/exchange 4.0 pair/spin/soc/dmi 2.6
-pair_coeff * * pair/spin/soc/dmi dmi 2.6 0.01 0.0 0.0 1.0 
+pair_coeff 	* * pair/spin/exchange exchange 4.0 0.0 0.003496 1.4885
-#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731 
+pair_coeff 	2 2 pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+#pair_coeff 	* * pair/spin/soc/dmi dmi 2.6 0.01 0.0 0.0 1.0 
+#pair_coeff 	* * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731 
 
-neighbor 0.1 bin
+neighbor 	0.1 bin
-neigh_modify every 10 check yes delay 20
+neigh_modify 	every 10 check yes delay 20
 
-fix 1 all force/spin anisotropy 0.0001 0.0 0.0 1.0
+fix 		1 fe_atoms force/spin anisotropy 0.0001 0.0 0.0 1.0
-fix 2 all langevin/spin 0.0 0.1 0.0 21
+fix 		2 all force/spin zeeman 0.1 0.0 0.0 1.0
-
+fix 		3 all langevin/spin 0.0 0.1 21
-fix 3 all integration/spin lattice no
+fix 		4 all integration/spin lattice no
 
 timestep	0.0002
 
 # define output and run
 
-compute out_mag    all compute/spin
+compute 	out_mag all compute/spin
-variable magz      equal c_out_mag[4]
+variable 	magz equal c_out_mag[4]
-variable magnorm   equal c_out_mag[5]
+variable 	magnorm equal c_out_mag[5]
-variable emag      equal c_out_mag[6]
+variable 	emag equal c_out_mag[6]
-variable tmag      equal c_out_mag[7]
+variable 	tmag equal c_out_mag[7]
-variable mag_force equal f_1
+variable 	mag_force equal f_1
 
 thermo_style    custom step time v_magnorm v_emag etotal
-thermo          50
+thermo          10
 
-dump 1 all custom 50 dump_skyrmion.lammpstrj type x y z spx spy spz
+dump 		1 all custom 50 dump_skyrmion.lammpstrj type x y z spx spy spz
 
-run 10000
+run 		1000
 

src/SPIN/fix_langevin_spin.cpp

@@ -51,7 +51,7 @@ using namespace MathConst;
 FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg), id_temp(NULL), random(NULL)
 {
-  if (narg != 7) error->all(FLERR,"Illegal langevin/spin command");
+  if (narg != 6) error->all(FLERR,"Illegal langevin/spin command");
 
   dynamic_group_allow = 1;
   scalar_flag = 1;
@@ -61,8 +61,7 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) :
 
   temp = force->numeric(FLERR,arg[3]);
   alpha_t = force->numeric(FLERR,arg[4]);
-  alpha_l = force->numeric(FLERR,arg[5]);
+  seed = force->inumeric(FLERR,arg[5]);
-  seed = force->inumeric(FLERR,arg[6]);
 
   if (alpha_t < 0.0) {
     error->all(FLERR,"Illegal langevin/spin command");
@@ -72,14 +71,6 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) :
     tdamp_flag = 1;
   }
 
-  if (alpha_l < 0.0) {
-    error->all(FLERR,"Illegal langevin/spin command");
-  } else if (alpha_l == 0.0) {
-    ldamp_flag = 0;
-  } else {
-    ldamp_flag = 1;
-  }
-  
   if (temp < 0.0) {
     error->all(FLERR,"Illegal langevin/spin command");
   } else if (temp == 0.0) {
@@ -119,7 +110,8 @@ int FixLangevinSpin::setmask()
 
 void FixLangevinSpin::init()
 {
-  // warn if any fix comes after this one  
+  // fix_langevin_spin has to be the last defined fix
+  
   int after = 0;
   int flag_force = 0;
   int flag_lang = 0;

src/SPIN/fix_langevin_spin.h

@@ -39,7 +39,7 @@ class FixLangevinSpin : public Fix {
 
  protected:
   double *spi, *fmi;
-  double alpha_t, alpha_l;	// transverse and longitudunal damping coeff. 
+  double alpha_t;		// transverse mag. damping
   double dts;        		// magnetic timestep
   double temp;       		// spin bath temperature
   double D,sigma;    		// bath intensity var.