Loading doc/src/fix_nh.rst +1 −1 Original line number Diff line number Diff line Loading @@ -132,7 +132,7 @@ integrators derived by Tuckerman et al in :ref:`(Tuckerman) <nh-Tuckerman>`. ---------- The thermostat parameters for fix styles *nvt* and *npt* is specified The thermostat parameters for fix styles *nvt* and *npt* are specified using the *temp* keyword. Other thermostat-related keywords are *tchain*\ , *tloop* and *drag*\ , which are discussed below. Loading doc/src/fix_npt_cauchy.rst +13 −13 Original line number Diff line number Diff line Loading @@ -47,7 +47,7 @@ Syntax *scalexz* value = *yes* or *no* = scale xz with lz *flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed *cauchystat* cauchystat values = alpha continue alpha = strength of Cauchystat control parameter alpha = strength of Cauchy stress control parameter continue = *yes* or *no* = whether of not to continue from a previous run *fixedpoint* values = x y z x,y,z = perform barostat dilation/contraction around this point (distance units) Loading Loading @@ -292,7 +292,7 @@ negligible. The keyword *tloop* can be used to improve the accuracy of integration scheme at little extra cost. The initial and final updates of the thermostat variables are broken up into *tloop* substeps, each of thermostat variables are broken up into *tloop* sub-steps, each of length *dt*\ /\ *tloop*\ . This corresponds to using a first-order Suzuki-Yoshida scheme :ref:`(Tuckerman) <nc-Tuckerman>`. The keyword *ploop* does the same thing for the barostat thermostat. Loading Loading @@ -358,7 +358,7 @@ The flip operation is described in more detail in the doc page for :doc:`fix deform <fix_deform>`. Both the barostat dynamics and the atom trajectories are unaffected by this operation. However, if a tilt factor is incremented by a large amount (1.5 times the box length) on a single timestep, LAMMPS can not accomodate this event and will a single timestep, LAMMPS can not accommodate this event and will terminate the simulation with an error. This error typically indicates that there is something badly wrong with how the simulation was constructed, such as specifying values of *Pstart* that are too far Loading Loading @@ -583,7 +583,7 @@ and if the tilt factor is not coupled to the barostat via keywords Without the *cauchystat* keyword, the barostat algorithm controls the Second-Piola Kirchhoff stress, which is a stress measure referred to the undeformed (initial) simulation box. If the box referred to the unmodified (initial) simulation box. If the box deforms substantially during the equilibration, the difference between the set values and the final true (Cauchy) stresses can be considerable. Loading @@ -591,7 +591,7 @@ considerable. The *cauchystat* keyword modifies the barostat as per Miller et al. (Miller)\_"#nc-Miller" so that the Cauchy stress is controlled. *alpha* is the non-dimensional parameter, typically set to 0.001 or 0.01 that determines how aggresively the algorithm drives the system 0.01 that determines how aggressively the algorithm drives the system towards the set Cauchy stresses. Larger values of *alpha* will modify the system more quickly, but can lead to instabilities. Smaller values will lead to longer convergence time. Since *alpha* also Loading @@ -599,20 +599,20 @@ influences how much the stress fluctuations deviate from the equilibrium fluctuations, it should be set as small as possible. A *continue* value of *yes* indicates that the fix is subsequent to a previous run with the Cauchystat fix, and the intention is to continue previous run with the npt/cauchy fix, and the intention is to continue from the converged stress state at the end of the previous run. This may be required, for example, when implementing a multi-step loading/unloading sequence over several fixes. Setting *alpha* to zero is not permitted. To "turn off" the Cauchystat control and thus restore the equilibrium stress cauchystat control and thus restore the equilibrium stress fluctuations, two subsequent fixes should be used. In the first, the Cauchystat is used and the simulation box equilibrates to the correct shape for the desired stresses. In the second, the *fix* statement is identical except that the *cauchystat* keyword is removed (along with related *alpha* and *continue* values). This restores the original Parrinello-Rahman algorithm, but now with the correct simulation box shape from the first fix. cauchystat flag is used and the simulation box equilibrates to the correct shape for the desired stresses. In the second, the *fix* statement is identical except that the *cauchystat* keyword is removed (along with related *alpha* and *continue* values). This restores the original Parrinello-Rahman algorithm, but now with the correct simulation box shape from the first fix. This fix can be used with dynamic groups as defined by the :doc:`group <group>` command. Likewise it can be used with groups to Loading doc/src/fix_npt_cauchy.txtdeleted 100644 → 0 +0 −612 File deleted.Preview size limit exceeded, changes collapsed. Show changes doc/utils/sphinx-config/false_positives.txt +5 −0 Original line number Diff line number Diff line Loading @@ -307,6 +307,8 @@ cartesian CasP Caswell Cates cauchy cauchystat Cavium Cawkwell cbecker Loading Loading @@ -773,6 +775,7 @@ equi equil equilibrate equilibrated equilibrates equilibrating equilibration Equilibria Loading Loading @@ -2115,6 +2118,7 @@ pathangle Patomtrans Pattnaik Pavese Pavia Paxton pbc pc Loading Loading @@ -2173,6 +2177,7 @@ piecewise Pieniazek Pieter pimd Piola Pisarev Pishevar Pitera Loading Loading
doc/src/fix_nh.rst +1 −1 Original line number Diff line number Diff line Loading @@ -132,7 +132,7 @@ integrators derived by Tuckerman et al in :ref:`(Tuckerman) <nh-Tuckerman>`. ---------- The thermostat parameters for fix styles *nvt* and *npt* is specified The thermostat parameters for fix styles *nvt* and *npt* are specified using the *temp* keyword. Other thermostat-related keywords are *tchain*\ , *tloop* and *drag*\ , which are discussed below. Loading
doc/src/fix_npt_cauchy.rst +13 −13 Original line number Diff line number Diff line Loading @@ -47,7 +47,7 @@ Syntax *scalexz* value = *yes* or *no* = scale xz with lz *flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed *cauchystat* cauchystat values = alpha continue alpha = strength of Cauchystat control parameter alpha = strength of Cauchy stress control parameter continue = *yes* or *no* = whether of not to continue from a previous run *fixedpoint* values = x y z x,y,z = perform barostat dilation/contraction around this point (distance units) Loading Loading @@ -292,7 +292,7 @@ negligible. The keyword *tloop* can be used to improve the accuracy of integration scheme at little extra cost. The initial and final updates of the thermostat variables are broken up into *tloop* substeps, each of thermostat variables are broken up into *tloop* sub-steps, each of length *dt*\ /\ *tloop*\ . This corresponds to using a first-order Suzuki-Yoshida scheme :ref:`(Tuckerman) <nc-Tuckerman>`. The keyword *ploop* does the same thing for the barostat thermostat. Loading Loading @@ -358,7 +358,7 @@ The flip operation is described in more detail in the doc page for :doc:`fix deform <fix_deform>`. Both the barostat dynamics and the atom trajectories are unaffected by this operation. However, if a tilt factor is incremented by a large amount (1.5 times the box length) on a single timestep, LAMMPS can not accomodate this event and will a single timestep, LAMMPS can not accommodate this event and will terminate the simulation with an error. This error typically indicates that there is something badly wrong with how the simulation was constructed, such as specifying values of *Pstart* that are too far Loading Loading @@ -583,7 +583,7 @@ and if the tilt factor is not coupled to the barostat via keywords Without the *cauchystat* keyword, the barostat algorithm controls the Second-Piola Kirchhoff stress, which is a stress measure referred to the undeformed (initial) simulation box. If the box referred to the unmodified (initial) simulation box. If the box deforms substantially during the equilibration, the difference between the set values and the final true (Cauchy) stresses can be considerable. Loading @@ -591,7 +591,7 @@ considerable. The *cauchystat* keyword modifies the barostat as per Miller et al. (Miller)\_"#nc-Miller" so that the Cauchy stress is controlled. *alpha* is the non-dimensional parameter, typically set to 0.001 or 0.01 that determines how aggresively the algorithm drives the system 0.01 that determines how aggressively the algorithm drives the system towards the set Cauchy stresses. Larger values of *alpha* will modify the system more quickly, but can lead to instabilities. Smaller values will lead to longer convergence time. Since *alpha* also Loading @@ -599,20 +599,20 @@ influences how much the stress fluctuations deviate from the equilibrium fluctuations, it should be set as small as possible. A *continue* value of *yes* indicates that the fix is subsequent to a previous run with the Cauchystat fix, and the intention is to continue previous run with the npt/cauchy fix, and the intention is to continue from the converged stress state at the end of the previous run. This may be required, for example, when implementing a multi-step loading/unloading sequence over several fixes. Setting *alpha* to zero is not permitted. To "turn off" the Cauchystat control and thus restore the equilibrium stress cauchystat control and thus restore the equilibrium stress fluctuations, two subsequent fixes should be used. In the first, the Cauchystat is used and the simulation box equilibrates to the correct shape for the desired stresses. In the second, the *fix* statement is identical except that the *cauchystat* keyword is removed (along with related *alpha* and *continue* values). This restores the original Parrinello-Rahman algorithm, but now with the correct simulation box shape from the first fix. cauchystat flag is used and the simulation box equilibrates to the correct shape for the desired stresses. In the second, the *fix* statement is identical except that the *cauchystat* keyword is removed (along with related *alpha* and *continue* values). This restores the original Parrinello-Rahman algorithm, but now with the correct simulation box shape from the first fix. This fix can be used with dynamic groups as defined by the :doc:`group <group>` command. Likewise it can be used with groups to Loading
doc/src/fix_npt_cauchy.txtdeleted 100644 → 0 +0 −612 File deleted.Preview size limit exceeded, changes collapsed. Show changes
doc/utils/sphinx-config/false_positives.txt +5 −0 Original line number Diff line number Diff line Loading @@ -307,6 +307,8 @@ cartesian CasP Caswell Cates cauchy cauchystat Cavium Cawkwell cbecker Loading Loading @@ -773,6 +775,7 @@ equi equil equilibrate equilibrated equilibrates equilibrating equilibration Equilibria Loading Loading @@ -2115,6 +2118,7 @@ pathangle Patomtrans Pattnaik Pavese Pavia Paxton pbc pc Loading Loading @@ -2173,6 +2177,7 @@ piecewise Pieniazek Pieter pimd Piola Pisarev Pishevar Pitera Loading
