diff --git a/examples/BORN_MATRIX/Analytical/born.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/born.out similarity index 100% rename from examples/BORN_MATRIX/Analytical/born.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/born.out diff --git a/examples/BORN_MATRIX/Analytical/born_matrix.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/born_matrix.out similarity index 100% rename from examples/BORN_MATRIX/Analytical/born_matrix.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/born_matrix.out diff --git a/examples/BORN_MATRIX/Analytical/compute_born.py b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py similarity index 100% rename from examples/BORN_MATRIX/Analytical/compute_born.py rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py diff --git a/examples/BORN_MATRIX/Analytical/full_matrix.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/full_matrix.out similarity index 100% rename from examples/BORN_MATRIX/Analytical/full_matrix.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/full_matrix.out diff --git a/examples/BORN_MATRIX/Analytical/in.ljcov b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/in.ljcov similarity index 100% rename from examples/BORN_MATRIX/Analytical/in.ljcov rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/in.ljcov diff --git a/examples/BORN_MATRIX/Analytical/stre_matrix.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/stre_matrix.out similarity index 100% rename from examples/BORN_MATRIX/Analytical/stre_matrix.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/stre_matrix.out diff --git a/examples/BORN_MATRIX/Analytical/temp_matrix.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/temp_matrix.out similarity index 100% rename from examples/BORN_MATRIX/Analytical/temp_matrix.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/temp_matrix.out diff --git a/examples/BORN_MATRIX/Analytical/vir.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/vir.out similarity index 100% rename from examples/BORN_MATRIX/Analytical/vir.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/vir.out diff --git a/examples/BORN_MATRIX/Numdiff/born.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/born.out similarity index 100% rename from examples/BORN_MATRIX/Numdiff/born.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/born.out diff --git a/examples/BORN_MATRIX/Numdiff/born_matrix.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/born_matrix.out similarity index 100% rename from examples/BORN_MATRIX/Numdiff/born_matrix.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/born_matrix.out diff --git a/examples/BORN_MATRIX/Numdiff/compute_born.py b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py similarity index 100% rename from examples/BORN_MATRIX/Numdiff/compute_born.py rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py diff --git a/examples/BORN_MATRIX/Numdiff/full_matrix.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/full_matrix.out similarity index 100% rename from examples/BORN_MATRIX/Numdiff/full_matrix.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/full_matrix.out diff --git a/examples/BORN_MATRIX/Numdiff/in.ljcov b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/in.ljcov similarity index 100% rename from examples/BORN_MATRIX/Numdiff/in.ljcov rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/in.ljcov diff --git a/examples/BORN_MATRIX/Numdiff/stre_matrix.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/stre_matrix.out similarity index 100% rename from examples/BORN_MATRIX/Numdiff/stre_matrix.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/stre_matrix.out diff --git a/examples/BORN_MATRIX/Numdiff/temp_matrix.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/temp_matrix.out similarity index 100% rename from examples/BORN_MATRIX/Numdiff/temp_matrix.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/temp_matrix.out diff --git a/examples/BORN_MATRIX/Numdiff/vir.out b/examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/vir.out similarity index 100% rename from examples/BORN_MATRIX/Numdiff/vir.out rename to examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/vir.out diff --git a/examples/BORN_MATRIX/README.md b/examples/ELASTIC_T/BORN_MATRIX/Argon/README.md similarity index 64% rename from examples/BORN_MATRIX/README.md rename to examples/ELASTIC_T/BORN_MATRIX/Argon/README.md index 606230c69a..c0a11af16f 100644 --- a/examples/BORN_MATRIX/README.md +++ b/examples/ELASTIC_T/BORN_MATRIX/Argon/README.md @@ -3,10 +3,11 @@ scripts creating argon fcc crystal and computing the Born term using the two methods described in the documentation. In the __Analytical__ directory the terms are computed using the analytical -derivation of the lj/cut pair style. +derivation of the Born term for the lj/cut pair style. -In the __Numdiff__ directory, the born term is evaluated through small +In the __Numdiff__ directory, the Born term is evaluated through small numerical differences of the stress tensor. This method can be used with any interaction potential. -Both script show examples on how to compute the full Cij tensor in LAMMPS. +Both script show examples on how to compute the full Cij elastic stiffness +tensor in LAMMPS. diff --git a/examples/ELASTIC_T/Si.sw b/examples/ELASTIC_T/DEFORMATION/Silicon/Si.sw similarity index 100% rename from examples/ELASTIC_T/Si.sw rename to examples/ELASTIC_T/DEFORMATION/Silicon/Si.sw diff --git a/examples/ELASTIC_T/displace.mod b/examples/ELASTIC_T/DEFORMATION/Silicon/displace.mod similarity index 100% rename from examples/ELASTIC_T/displace.mod rename to examples/ELASTIC_T/DEFORMATION/Silicon/displace.mod diff --git a/examples/ELASTIC_T/in.elastic b/examples/ELASTIC_T/DEFORMATION/Silicon/in.elastic similarity index 100% rename from examples/ELASTIC_T/in.elastic rename to examples/ELASTIC_T/DEFORMATION/Silicon/in.elastic diff --git a/examples/ELASTIC_T/init.mod b/examples/ELASTIC_T/DEFORMATION/Silicon/init.mod similarity index 100% rename from examples/ELASTIC_T/init.mod rename to examples/ELASTIC_T/DEFORMATION/Silicon/init.mod diff --git a/examples/ELASTIC_T/potential.mod b/examples/ELASTIC_T/DEFORMATION/Silicon/potential.mod similarity index 93% rename from examples/ELASTIC_T/potential.mod rename to examples/ELASTIC_T/DEFORMATION/Silicon/potential.mod index d4b7cc7158..7cd996d5d5 100644 --- a/examples/ELASTIC_T/potential.mod +++ b/examples/ELASTIC_T/DEFORMATION/Silicon/potential.mod @@ -2,7 +2,7 @@ # See in.elastic for more info. # we must undefine any fix ave/* fix before using reset_timestep -if "$(is_defined(fix,avp)" then "unfix avp" +if "$(is_defined(fix,avp))" then "unfix avp" reset_timestep 0 # Choose potential diff --git a/examples/README b/examples/README index 92c723631c..f0396730a6 100644 --- a/examples/README +++ b/examples/README @@ -152,12 +152,19 @@ either by itself or in tandem with another code or library. See the COUPLE/README file to get started. The ELASTIC directory has an example script for computing elastic -constants at zero temperature, using an Si example. See the +stiffness tensor (elastic constants) +at zero temperature, using an Si example. See the ELASTIC/in.elastic file for more info. -The ELASTIC_T directory has an example script for computing elastic -constants at finite temperature, using an Si example. See the -ELASTIC_T/in.elastic file for more info. +The ELASTIC_T directory has example scripts for the computing elastic +stiffness tensor at finite temperature. Two different methods are +demonstrated. DEFORMATION estimates the change in the average +stress tensor between multiple simulations +in which small finite deformations are made to the simulation cell. +BORN_MATRIX runs a single simulation in which the Born matrix and stress +fluctuations are averaged. The second method +is newer in LAMMPS and is generally more efficient and +more reliable. The HEAT directory has example scripts for heat exchange algorithms (e.g. used for establishing a thermal gradient), using two different