From d4861e71d29418e51fb896f9386fe8701f64aa29 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 18 Jun 2018 18:36:30 -0400
Subject: [PATCH] integrate SPIN package into documentation, fix links and make
it consistent
---
doc/src/Section_commands.txt | 8 ++++++++
doc/src/computes.txt | 1 +
doc/src/fix_langevin_spin.txt | 17 ++++++++--------
doc/src/fixes.txt | 3 +++
doc/src/lammps.book | 8 ++++++++
doc/src/pair_spin_exchange.txt | 20 +++++++++----------
...pair_spin_me.txt => pair_spin_magelec.txt} | 20 +++++++++----------
doc/src/pairs.txt | 4 ++++
doc/src/tutorials.txt | 1 -
src/SPIN/pair_spin.cpp | 0
src/SPIN/pair_spin.h | 0
src/SPIN/pair_spin_dmi.cpp | 0
src/SPIN/pair_spin_dmi.h | 0
src/SPIN/pair_spin_exchange.cpp | 0
src/SPIN/pair_spin_exchange.h | 0
src/SPIN/pair_spin_magelec.cpp | 0
src/SPIN/pair_spin_magelec.h | 0
src/SPIN/pair_spin_neel.cpp | 0
src/SPIN/pair_spin_neel.h | 0
19 files changed, 52 insertions(+), 30 deletions(-)
rename doc/src/{pair_spin_me.txt => pair_spin_magelec.txt} (86%)
mode change 100755 => 100644 src/SPIN/pair_spin.cpp
mode change 100755 => 100644 src/SPIN/pair_spin.h
mode change 100755 => 100644 src/SPIN/pair_spin_dmi.cpp
mode change 100755 => 100644 src/SPIN/pair_spin_dmi.h
mode change 100755 => 100644 src/SPIN/pair_spin_exchange.cpp
mode change 100755 => 100644 src/SPIN/pair_spin_exchange.h
mode change 100755 => 100644 src/SPIN/pair_spin_magelec.cpp
mode change 100755 => 100644 src/SPIN/pair_spin_magelec.h
mode change 100755 => 100644 src/SPIN/pair_spin_neel.cpp
mode change 100755 => 100644 src/SPIN/pair_spin_neel.h
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 3dabdbeaa1..ef830951e6 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -583,6 +583,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"indent"_fix_indent.html,
"latte"_fix_latte.html,
"langevin (k)"_fix_langevin.html,
+"langevin/spin"_fix_langevin_spin.hmtl,
"lineforce"_fix_lineforce.html,
"momentum (k)"_fix_momentum.html,
"move"_fix_move.html,
@@ -606,6 +607,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"nve/line"_fix_nve_line.html,
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere (o)"_fix_nve_sphere.html,
+"nve/spin"_fix_nve_spin.html,
"nve/tri"_fix_nve_tri.html,
"nvt (iko)"_fix_nh.html,
"nvt/asphere (o)"_fix_nvt_asphere.html,
@@ -618,6 +620,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"planeforce"_fix_planeforce.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
+"precession/spin"_fix_precession_spin.html,
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"property/atom (k)"_fix_property_atom.html,
@@ -824,6 +827,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"sna/atom"_compute_sna_atom.html,
"snad/atom"_compute_sna_atom.html,
"snav/atom"_compute_sna_atom.html,
+"spin"_compute_spin.html,
"stress/atom"_compute_stress_atom.html,
"temp (k)"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
@@ -1017,6 +1021,10 @@ KOKKOS, o = USER-OMP, t = OPT.
"snap (k)"_pair_snap.html,
"soft (go)"_pair_soft.html,
"sw (giko)"_pair_sw.html,
+"spin/dmi"_pair_spin_dmi.html,
+"spin/exchange"_pair_spin_exchange.html,
+"spin/magelec"_pair_spin_magelec.html,
+"spin/neel"_pair_spin_neel.html,
"table (gko)"_pair_table.html,
"tersoff (giko)"_pair_tersoff.html,
"tersoff/mod (gko)"_pair_tersoff_mod.html,
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index 1b64e2e5b4..12de3e2788 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -95,6 +95,7 @@ Computes :h1
compute_smd_ulsph_stress
compute_smd_vol
compute_sna_atom
+ compute_spin
compute_stress_atom
compute_tally
compute_tdpd_cc_atom
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index 246ee02331..51f085ebdc 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -27,7 +27,7 @@ fix 2 all langevin/spin 300.0 0.01 21 :pre
Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the
magnetic spins associated to the atoms.
-Used with "fix integration spin"_fix_integration_spin.html, this command performs
+Used with "fix nve/spin"_fix_nve_spin.html, this command performs
Brownian dynamics (BD).
A random torque and a transverse dissipation are applied to each spin i according to
the following stochastic differential equation:
@@ -48,9 +48,9 @@ Note: due to the form of the sLLG equation, this fix has to be defined just
before the nve/spin fix (and after all other magnetic fixes).
As an example:
-fix 1 all force/spin zeeman 0.01 0.0 0.0 1.0
+fix 1 all precession/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
+fix 3 all nve/spin lattice yes :pre
is correct, but defining a force/spin command after the langevin/spin command
would give an error message.
@@ -80,16 +80,15 @@ The {langevin/spin} fix is part of the SPIN package.
This style is only enabled if LAMMPS was built with this package.
See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
-The numerical integration has to be performed with {fix/nve/spin}
-when {langevin/spin} is enabled.
+The numerical integration has to be performed with {fix nve/spin}
+when {fix 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).
+This fix has to be the last defined magnetic fix before the time
+integration fix (e.g. {fix nve/spin}).
[Related commands:]
-"fix integration spin"_fix_integration_spin.html,
-"pair spin"_pair_spin.html
+"fix nve/spin"_fix_nve_spin.html, "fix precession/spin"_fix_precession_spin.html
[Default:] none
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index 79c2f75b8b..9510217d02 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -61,6 +61,7 @@ Fixes :h1
fix_langevin
fix_langevin_drude
fix_langevin_eff
+ fix_langevin_spin
fix_latte
fix_lb_fluid
fix_lb_momentum
@@ -99,6 +100,7 @@ Fixes :h1
fix_nve_manifold_rattle
fix_nve_noforce
fix_nve_sphere
+ fix_nve_spin
fix_nve_tri
fix_nvk
fix_nvt_asphere
@@ -114,6 +116,7 @@ Fixes :h1
fix_planeforce
fix_poems
fix_pour
+ fix_precession_spin
fix_press_berendsen
fix_print
fix_property_atom
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 0764c593f7..22be6c7f53 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -176,6 +176,7 @@ fix_ipi.html
fix_langevin.html
fix_langevin_drude.html
fix_langevin_eff.html
+fix_langevin_spin.html
fix_latte.html
fix_lb_fluid.html
fix_lb_momentum.html
@@ -213,6 +214,7 @@ fix_nve_line.html
fix_nve_manifold_rattle.html
fix_nve_noforce.html
fix_nve_sphere.html
+fix_nve_spin.html
fix_nve_tri.html
fix_nvk.html
fix_nvt_asphere.html
@@ -229,6 +231,7 @@ fix_pimd.html
fix_planeforce.html
fix_poems.html
fix_pour.html
+fix_precession_spin.html
fix_press_berendsen.html
fix_print.html
fix_property_atom.html
@@ -381,6 +384,7 @@ compute_smd_ulsph_strain_rate.html
compute_smd_ulsph_stress.html
compute_smd_vol.html
compute_sna_atom.html
+compute_spin.html
compute_stress_atom.html
compute_tally.html
compute_tdpd_cc_atom.html
@@ -506,6 +510,10 @@ pair_sph_lj.html
pair_sph_rhosum.html
pair_sph_taitwater.html
pair_sph_taitwater_morris.html
+pair_spin_dmi.html
+pair_spin_exchange.html
+pair_spin_magelec.html
+pair_spin_neel.html
pair_srp.html
pair_sw.html
pair_table.html
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
index 90a75705c7..97b6d0b34f 100644
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@@ -15,42 +15,42 @@ pair_style spin/exchange cutoff :pre
cutoff = global cutoff pair (distance in metal units) :ulb,l
:ule
-
+
[Examples:]
-pair_style spin/exchange 4.0
+pair_style spin/exchange 4.0
pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre
[Description:]
Style {spin/exchange} computes the exchange interaction between
-pairs of magnetic spins:
+pairs of magnetic spins:
:c,image(Eqs/pair_spin_exchange_interaction.jpg)
where si and sj are two neighboring magnetic spins of two particles,
rij = ri - rj is the inter-atomic distance between the two particles,
and J(rij) is a function defining the intensity and the sign of the exchange
-interaction.
+interaction.
This function is defined as:
:c,image(Eqs/pair_spin_exchange_function.jpg)
-where a, b and d are the three constant coefficients defined in the associated
-"pair_coeff" command.
+where a, b and d are the three constant coefficients defined in the associated
+"pair_coeff" command.
-The coefficients a, b, and d need to be fitted so that the function above matches with
+The coefficients a, b, and d need to be fitted so that the function above matches with
the value of the exchange interaction for the N neighbor shells taken into account.
-Examples and more explanations about this function and its parametrization are reported
+Examples and more explanations about this function and its parametrization are reported
in "(Tranchida)"_#Tranchida3.
From this exchange interaction, each spin i will be submitted
to a magnetic torque omega, and its associated atom can be submitted to a
-force F for spin-lattice calculations (see
-"fix_integration_spin"_fix_integration_spin.html), such as:
+force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html),
+such as:
:c,image(Eqs/pair_spin_exchange_forces.jpg)
diff --git a/doc/src/pair_spin_me.txt b/doc/src/pair_spin_magelec.txt
similarity index 86%
rename from doc/src/pair_spin_me.txt
rename to doc/src/pair_spin_magelec.txt
index 8186775b77..0185a5abb2 100644
--- a/doc/src/pair_spin_me.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -15,7 +15,7 @@ pair_style spin/me cutoff :pre
cutoff = global cutoff pair (distance in metal units) :ulb,l
:ule
-
+
[Examples:]
pair_style spin/me 4.5
@@ -29,16 +29,16 @@ pairs of magnetic spins. According to the derivation reported in
:c,image(Eqs/pair_spin_me_interaction.jpg)
-where si and sj are neighboring magnetic spins of two particles,
-eij = (ri - rj)/|ri-rj| is the normalized separation vector between the
+where si and sj are neighboring magnetic spins of two particles,
+eij = (ri - rj)/|ri-rj| is the normalized separation vector between the
two particles, and E is an electric polarization vector.
-The norm and direction of E are giving the intensity and the
+The norm and direction of E are giving the intensity and the
direction of a screened dielectric atomic polarization (in eV).
-From this magneto-electric interaction, each spin i will be submitted
+From this magneto-electric interaction, each spin i will be submitted
to a magnetic torque omega, and its associated atom can be submitted to a
-force F for spin-lattice calculations (see
-"fix_integration_spin"_fix_integration_spin.html), such as:
+force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html),
+such as:
:c,image(Eqs/pair_spin_me_forces.jpg)
@@ -51,14 +51,14 @@ More details about the derivation of these torques/forces are reported in
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
+All the {pair/spin} styles are part of the SPIN package.
These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
+if the atom_style "spin" was declared.
See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
-"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
+"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html,
"pair_spin_exchange"_pair_spin_exchange.html, "pair_eam"_pair_eam.html,
[Default:] none
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 202aaa9c0f..1a5e98a109 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -97,6 +97,10 @@ Pair Styles :h1
pair_sph_rhosum
pair_sph_taitwater
pair_sph_taitwater_morris
+ pair_spin_dmi
+ pair_spin_exchange
+ pair_spin_magelec
+ pair_spin_neel
pair_srp
pair_sw
pair_table
diff --git a/doc/src/tutorials.txt b/doc/src/tutorials.txt
index 97e7883841..338439ac8e 100644
--- a/doc/src/tutorials.txt
+++ b/doc/src/tutorials.txt
@@ -9,7 +9,6 @@ Tutorials :h1
tutorial_github
tutorial_pylammps
tutorial_bash_on_windows
- tutorial_spin
body
manifolds
diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp
old mode 100755
new mode 100644
diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h
old mode 100755
new mode 100644
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
old mode 100755
new mode 100644
diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h
old mode 100755
new mode 100644
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
old mode 100755
new mode 100644
diff --git a/src/SPIN/pair_spin_exchange.h b/src/SPIN/pair_spin_exchange.h
old mode 100755
new mode 100644
diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp
old mode 100755
new mode 100644
diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h
old mode 100755
new mode 100644
diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp
old mode 100755
new mode 100644
diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h
old mode 100755
new mode 100644
--
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