Loading doc/src/fix_neb.txt +11 −12 Original line number Diff line number Diff line Loading @@ -34,7 +34,7 @@ keyword = {nudge} or {perp} or {ends} :l fix 1 active neb 10.0 fix 2 all neb 1.0 perp 1.0 end last fix 2 all neb 1.0 perp 1.0 end first end last fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0 fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre [Description:] Loading Loading @@ -64,7 +64,7 @@ Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fspring_perp :pre T' is the unit "tangent" vector for replica I and is a function of Ri, Ri-1, Ri+1, and the potential energy of the 3 replicas; it points roughly in the direction of (Ri+i - Ri-1); see the "(Henkelman1)"_#Henkelman1 paper for details. Ri are the atomic "(Henkelman1)"_#Henkelman1 paper for details. Ri gives the atomic coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its neighbor replicas. The term (Grad(V) dot T') is used to remove the component of the gradient parallel to the path which would tend to Loading Loading @@ -114,7 +114,7 @@ keeping the replicas equally spaced. :line The keyword {perp} adds a spring force perpendicular to the path in order to prevent the path from becoming too kinky, with magnitude It order to prevent the path from becoming too kinky. It can significantly improve the convergence of the NEB calculation when the resolution is poor. I.e. when too few replicas are used; see "(Maras)"_#Maras1 for details. Loading @@ -133,11 +133,11 @@ force is added. :line By default, no forces act on the first and last replicas during the NEB relaxation, so these replicas simply relax toward their respective local minima. By using the key word {end}, additional forces can be applied to the first or last replica, to enable them to relax toward a MEP while constraining their energy. By default, no nudging forces act on the first and last replicas during the NEB relaxation, so these replicas simply relax toward their respective local minima. By using the key word {end}, additional forces can be applied to the first or last replica, to enable them to relax toward a MEP while constraining their energy. The interatomic force Fi for the specified replica becomes: Loading Loading @@ -177,10 +177,9 @@ only be done if a particular intermediate replica has a lower energy than the first replica. This should effectively prevent the intermediate replicas from over-relaxing. After converging a NEB calculation using an {estyle} of {last/efirst}, you should check that all intermediate replicas have a larger energy than the first replica. If not, then repeat the calculation with an {estyle} of {last/efirst/middle}. After converging a NEB calculation using an {estyle} of {last/efirst/middle}, you should check that all intermediate replicas have a larger energy than the first replica. If this is not the case, the path is probably not a MEP. Finally, note that if the last replica converges toward a local minimum which has a larger energy than the energy of the first Loading examples/neb/README +2 −2 Original line number Diff line number Diff line Loading @@ -2,12 +2,12 @@ Run these examples as: mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1 mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2 mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1freeend mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1.end mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1 mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2 mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1freeend mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1.end mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac Loading examples/neb/in.neb.hop2 +1 −1 Original line number Diff line number Diff line Loading @@ -65,4 +65,4 @@ thermo 100 min_style fire neb 0.0 0.01 1000 1000 100 final final.hop2 neb 0.0 0.05 1000 1000 100 final final.hop2 examples/neb/log.19June17.neb.hop1.end.g++.4 0 → 100644 +11 −0 Original line number Diff line number Diff line LAMMPS (19 May 2017) Running on 4 partitions of processors Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN 0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928 100 0.11027532 0.085410308 3.0967938 0.024201563 0.38551033 0.0017583261 0.0021866943 1.7710358 0 -3.0483469 0.31192818 -3.0465886 0.61093022 -3.0466143 1 -3.0487752 130 0.09954083 0.075481108 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776 Climbing replica = 2 Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN 130 0.37838747 0.3502435 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776 230 0.22757286 0.12027481 3.1250243 0.0081260569 0.14019507 0.0018364585 0.002278918 1.76926 0 -3.0483347 0.39730698 -3.0464983 0.64450769 -3.0466973 1 -3.0487772 278 0.096184498 0.085088496 3.1405655 0.0068164307 0.093861113 0.0018426056 0.002286256 1.7684765 0 -3.0483338 0.41277997 -3.0464912 0.65562984 -3.0467294 1 -3.0487775 examples/neb/log.19June17.neb.hop1.end.g++.8 0 → 100644 +11 −0 Original line number Diff line number Diff line LAMMPS (19 May 2017) Running on 4 partitions of processors Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN 0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928 100 0.11375359 0.085350745 3.0966418 0.0236765 0.38531777 0.0017582606 0.0021868783 1.7710738 0 -3.0483467 0.31201141 -3.0465884 0.61117406 -3.0466149 1 -3.0487753 119 0.09996986 0.078639268 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758 Climbing replica = 2 Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN 119 0.3793192 0.35281863 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758 219 0.20159133 0.12247026 3.1244061 0.0085896057 0.13938632 0.0018362816 0.0022783681 1.7693295 0 -3.048335 0.39646633 -3.0464988 0.64277703 -3.0466925 1 -3.0487771 266 0.099868725 0.086180598 3.1401661 0.0070922949 0.095128081 0.001842608 0.002286044 1.7685191 0 -3.048334 0.41231024 -3.0464914 0.65425179 -3.0467252 1 -3.0487774 Loading
doc/src/fix_neb.txt +11 −12 Original line number Diff line number Diff line Loading @@ -34,7 +34,7 @@ keyword = {nudge} or {perp} or {ends} :l fix 1 active neb 10.0 fix 2 all neb 1.0 perp 1.0 end last fix 2 all neb 1.0 perp 1.0 end first end last fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0 fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre [Description:] Loading Loading @@ -64,7 +64,7 @@ Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fspring_perp :pre T' is the unit "tangent" vector for replica I and is a function of Ri, Ri-1, Ri+1, and the potential energy of the 3 replicas; it points roughly in the direction of (Ri+i - Ri-1); see the "(Henkelman1)"_#Henkelman1 paper for details. Ri are the atomic "(Henkelman1)"_#Henkelman1 paper for details. Ri gives the atomic coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its neighbor replicas. The term (Grad(V) dot T') is used to remove the component of the gradient parallel to the path which would tend to Loading Loading @@ -114,7 +114,7 @@ keeping the replicas equally spaced. :line The keyword {perp} adds a spring force perpendicular to the path in order to prevent the path from becoming too kinky, with magnitude It order to prevent the path from becoming too kinky. It can significantly improve the convergence of the NEB calculation when the resolution is poor. I.e. when too few replicas are used; see "(Maras)"_#Maras1 for details. Loading @@ -133,11 +133,11 @@ force is added. :line By default, no forces act on the first and last replicas during the NEB relaxation, so these replicas simply relax toward their respective local minima. By using the key word {end}, additional forces can be applied to the first or last replica, to enable them to relax toward a MEP while constraining their energy. By default, no nudging forces act on the first and last replicas during the NEB relaxation, so these replicas simply relax toward their respective local minima. By using the key word {end}, additional forces can be applied to the first or last replica, to enable them to relax toward a MEP while constraining their energy. The interatomic force Fi for the specified replica becomes: Loading Loading @@ -177,10 +177,9 @@ only be done if a particular intermediate replica has a lower energy than the first replica. This should effectively prevent the intermediate replicas from over-relaxing. After converging a NEB calculation using an {estyle} of {last/efirst}, you should check that all intermediate replicas have a larger energy than the first replica. If not, then repeat the calculation with an {estyle} of {last/efirst/middle}. After converging a NEB calculation using an {estyle} of {last/efirst/middle}, you should check that all intermediate replicas have a larger energy than the first replica. If this is not the case, the path is probably not a MEP. Finally, note that if the last replica converges toward a local minimum which has a larger energy than the energy of the first Loading
examples/neb/README +2 −2 Original line number Diff line number Diff line Loading @@ -2,12 +2,12 @@ Run these examples as: mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1 mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2 mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1freeend mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1.end mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1 mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2 mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1freeend mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1.end mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac Loading
examples/neb/in.neb.hop2 +1 −1 Original line number Diff line number Diff line Loading @@ -65,4 +65,4 @@ thermo 100 min_style fire neb 0.0 0.01 1000 1000 100 final final.hop2 neb 0.0 0.05 1000 1000 100 final final.hop2
examples/neb/log.19June17.neb.hop1.end.g++.4 0 → 100644 +11 −0 Original line number Diff line number Diff line LAMMPS (19 May 2017) Running on 4 partitions of processors Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN 0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928 100 0.11027532 0.085410308 3.0967938 0.024201563 0.38551033 0.0017583261 0.0021866943 1.7710358 0 -3.0483469 0.31192818 -3.0465886 0.61093022 -3.0466143 1 -3.0487752 130 0.09954083 0.075481108 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776 Climbing replica = 2 Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN 130 0.37838747 0.3502435 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776 230 0.22757286 0.12027481 3.1250243 0.0081260569 0.14019507 0.0018364585 0.002278918 1.76926 0 -3.0483347 0.39730698 -3.0464983 0.64450769 -3.0466973 1 -3.0487772 278 0.096184498 0.085088496 3.1405655 0.0068164307 0.093861113 0.0018426056 0.002286256 1.7684765 0 -3.0483338 0.41277997 -3.0464912 0.65562984 -3.0467294 1 -3.0487775
examples/neb/log.19June17.neb.hop1.end.g++.8 0 → 100644 +11 −0 Original line number Diff line number Diff line LAMMPS (19 May 2017) Running on 4 partitions of processors Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN 0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928 100 0.11375359 0.085350745 3.0966418 0.0236765 0.38531777 0.0017582606 0.0021868783 1.7710738 0 -3.0483467 0.31201141 -3.0465884 0.61117406 -3.0466149 1 -3.0487753 119 0.09996986 0.078639268 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758 Climbing replica = 2 Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN 119 0.3793192 0.35281863 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758 219 0.20159133 0.12247026 3.1244061 0.0085896057 0.13938632 0.0018362816 0.0022783681 1.7693295 0 -3.048335 0.39646633 -3.0464988 0.64277703 -3.0466925 1 -3.0487771 266 0.099868725 0.086180598 3.1401661 0.0070922949 0.095128081 0.001842608 0.002286044 1.7685191 0 -3.048334 0.41231024 -3.0464914 0.65425179 -3.0467252 1 -3.0487774
