ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

fix of style related issues

Browse Source
This commit is contained in:
iafoss
2020-02-07 13:29:05 -05:00
parent 0204bf286b
commit 8c82c60f2f
24 changed files with 71 additions and 71 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
doc/src/compute_cnt.rst
View File

@ -13,13 +13,13 @@ compute cnt/B command
======================= =======================
compute cnt/Es\_tot command compute cnt/Es\_tot command
======================= ============================
compute cnt/Eb\_tot command compute cnt/Eb\_tot command
======================= ============================
compute cnt/Et\_tot command compute cnt/Et\_tot command
======================= ============================
Syntax Syntax
"""""" """"""

6
doc/src/pair_cnt_tpm.rst
View File

@ -1,7 +1,7 @@
.. index:: pair\_style cnt/tpm .. index:: pair\_style cnt/tpm
pair\_style cnt/tpm command pair\_style cnt/tpm command
========================== ============================
Syntax Syntax
"""""" """"""
@ -34,8 +34,8 @@ simulations of interacting flexible nanotubes. The force field is based on the
mesoscopic computational model suggested in Ref. :ref:`[1] <Srivastava>`. mesoscopic computational model suggested in Ref. :ref:`[1] <Srivastava>`.
In this model, each nanotube is represented by a chain of mesoscopic elements In this model, each nanotube is represented by a chain of mesoscopic elements
in the form of stretchable cylindrical segments, where each segment consists in the form of stretchable cylindrical segments, where each segment consists
of multiple atoms. Each nanotube is divided into segments by a sequent of nodes of multiple atoms. Each nanotube is divided into segments by a sequence of
placed on the nanotube centerline. This sequence of nodes determines the nodes placed on the nanotube centerline. This sequence of nodes determines the
spatial position of the cylindrical segments and defines the configuration of spatial position of the cylindrical segments and defines the configuration of
the entire tube. the entire tube.

16
src/USER-CNT/atom_vec_cnt.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -84,7 +84,7 @@ void AtomVecCNT::grow_reset()
tag = atom->tag; type = atom->type; tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image; mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f; x = atom->x; v = atom->v; f = atom->f;
rmass = atom->rmass; rmass = atom->rmass;
radius = atom->radius; radius = atom->radius;
length = atom->length; length = atom->length;
@ -109,7 +109,7 @@ void AtomVecCNT::copy(int i, int j, int delflag)
v[j][0] = v[i][0]; v[j][0] = v[i][0];
v[j][1] = v[i][1]; v[j][1] = v[i][1];
v[j][2] = v[i][2]; v[j][2] = v[i][2];
rmass[j] = rmass[i]; rmass[j] = rmass[i];
radius[j] = radius[i]; radius[j] = radius[i];
length[j] = length[i]; length[j] = length[i];
@ -304,7 +304,7 @@ int AtomVecCNT::pack_border(int n, int *list, double *buf,
buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d; buf[m++] = ubuf(mask[j]).d;
buf[m++] = rmass[j]; buf[m++] = rmass[j];
buf[m++] = radius[j]; buf[m++] = radius[j];
buf[m++] = length[j]; buf[m++] = length[j];
@ -331,7 +331,7 @@ int AtomVecCNT::pack_border(int n, int *list, double *buf,
buf[m++] = ubuf(tag[j]).d; buf[m++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d; buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d; buf[m++] = ubuf(mask[j]).d;
buf[m++] = rmass[j]; buf[m++] = rmass[j];
buf[m++] = radius[j]; buf[m++] = radius[j];
buf[m++] = length[j]; buf[m++] = length[j];
@ -861,10 +861,10 @@ void AtomVecCNT::write_data(FILE *fp, int n, double **buf)
{ {
for (int i = 0; i < n; i++) for (int i = 0; i < n; i++)
fprintf(fp, TAGINT_FORMAT " " TAGINT_FORMAT " %d " fprintf(fp, TAGINT_FORMAT " " TAGINT_FORMAT " %d "
TAGINT_FORMAT " " TAGINT_FORMAT TAGINT_FORMAT " " TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %d %-1.16e %-1.16e %-1.16e %d %d %d\n", " %-1.16e %-1.16e %-1.16e %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i, (tagint) ubuf(buf[i][1]).i, (tagint) ubuf(buf[i][0]).i, (tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i, (tagint) ubuf(buf[i][3]).i, (int) ubuf(buf[i][2]).i, (tagint) ubuf(buf[i][3]).i,
(tagint) ubuf(buf[i][4]).i, (tagint) ubuf(buf[i][4]).i,
buf[i][5], buf[i][6], buf[i][7], (int) ubuf(buf[i][8]).i, buf[i][5], buf[i][6], buf[i][7], (int) ubuf(buf[i][8]).i,
buf[i][9], buf[i][10], buf[i][11], buf[i][9], buf[i][10], buf[i][11],
@ -878,7 +878,7 @@ void AtomVecCNT::write_data(FILE *fp, int n, double **buf)
int AtomVecCNT::write_data_hybrid(FILE *fp, double *buf) int AtomVecCNT::write_data_hybrid(FILE *fp, double *buf)
{ {
fprintf(fp," " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT fprintf(fp," " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
" %-1.16e %-1.16e %-1.16e %d", " %-1.16e %-1.16e %-1.16e %d",
(tagint) ubuf(buf[0]).i, (tagint) ubuf(buf[1]).i, (tagint) ubuf(buf[2]).i, (tagint) ubuf(buf[0]).i, (tagint) ubuf(buf[1]).i, (tagint) ubuf(buf[2]).i,
buf[3], buf[4], buf[5], (int)ubuf(buf[6]).i); buf[3], buf[4], buf[5], (int)ubuf(buf[6]).i);

6
src/USER-CNT/atom_vec_cnt.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -43,8 +43,8 @@ class AtomVecCNT : public AtomVec {
virtual int pack_border_vel(int, int *, double *, int, int *); virtual int pack_border_vel(int, int *, double *, int, int *);
virtual void unpack_border(int, int, double *); virtual void unpack_border(int, int, double *);
virtual void unpack_border_vel(int, int, double *); virtual void unpack_border_vel(int, int, double *);
int pack_border_hybrid(int, int *, double *); int pack_border_hybrid(int, int *, double *);
int unpack_border_hybrid(int, int, double *); int unpack_border_hybrid(int, int, double *);
virtual int pack_exchange(int, double *); virtual int pack_exchange(int, double *);
virtual int unpack_exchange(double *); virtual int unpack_exchange(double *);
int size_restart(); int size_restart();

16
src/USER-CNT/cntlist.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -18,7 +18,7 @@
#include <cmath> #include <cmath>
template<typename T> template<typename T>
void vector_union(std::vector<T>& v1, std::vector<T>& v2, void vector_union(std::vector<T>& v1, std::vector<T>& v2,
std::vector<T>& merged) { std::vector<T>& merged) {
std::sort(v1.begin(), v1.end()); std::sort(v1.begin(), v1.end());
std::sort(v2.begin(), v2.end()); std::sort(v2.begin(), v2.end());
@ -103,13 +103,13 @@ CNTList::CNTList(const Atom* atom, const NeighList* nblist, double rc2){
if (chain_list[i][0] != cnt_end && chain_list[i][0] != domain_end && if (chain_list[i][0] != cnt_end && chain_list[i][0] != domain_end &&
g_id[i] < g_id[chain_list[i][0]]){ g_id[i] < g_id[chain_list[i][0]]){
array2003<int, 2> tmp_c; array2003<int, 2> tmp_c;
tmp_c[0] = i; tmp_c[1] = chain_list[i][0]; tmp_c[0] = i; tmp_c[1] = chain_list[i][0];
segments.push_back(tmp_c); segments.push_back(tmp_c);
} }
if (chain_list[i][1] != cnt_end && chain_list[i][1] != domain_end && if (chain_list[i][1] != cnt_end && chain_list[i][1] != domain_end &&
g_id[i] < g_id[chain_list[i][1]]){ g_id[i] < g_id[chain_list[i][1]]){
array2003<int, 2> tmp_c; array2003<int, 2> tmp_c;
tmp_c[0] = i; tmp_c[1] = chain_list[i][1]; tmp_c[0] = i; tmp_c[1] = chain_list[i][1];
segments.push_back(tmp_c); segments.push_back(tmp_c);
} }
} }
@ -146,22 +146,22 @@ CNTList::CNTList(const Atom* atom, const NeighList* nblist, double rc2){
if (nnb > 0) { if (nnb > 0) {
int idx_s = nb_list[0]; int idx_s = nb_list[0];
for (int j = 0; j < nnb; j++) { for (int j = 0; j < nnb; j++) {
//if nodes are not continous in the sorted representation //if nodes are not continous in the sorted representation
//or represent chain ends, create a new neighbor chain //or represent chain ends, create a new neighbor chain
int idx_next = chain_list[index_list[nb_list[j]]][1]; int idx_next = chain_list[index_list[nb_list[j]]][1];
if ((j == nnb - 1) || (nb_list[j] + 1 != nb_list[j+1]) || if ((j == nnb - 1) || (nb_list[j] + 1 != nb_list[j+1]) ||
(idx_next == cnt_end) || (idx_next == domain_end)) { (idx_next == cnt_end) || (idx_next == domain_end)) {
int idx_f = nb_list[j]; int idx_f = nb_list[j];
array2003<int, 2> chain; array2003<int, 2> chain;
chain[0] = idx_s; chain[0] = idx_s;
chain[1] = nb_list[j]; chain[1] = nb_list[j];
//make sure that segments having at least one node //make sure that segments having at least one node
//in the neighbor list are included //in the neighbor list are included
int idx0 = index_list[chain[0]]; // real id of the ends int idx0 = index_list[chain[0]]; // real id of the ends
int idx1 = index_list[chain[1]]; int idx1 = index_list[chain[1]];
if (chain_list[idx0][0] != cnt_end && if (chain_list[idx0][0] != cnt_end &&
chain_list[idx0][0] != domain_end) chain[0] -= 1; chain_list[idx0][0] != domain_end) chain[0] -= 1;
if (chain_list[idx1][1] != cnt_end && if (chain_list[idx1][1] != cnt_end &&
chain_list[idx1][1] != domain_end) chain[1] += 1; chain_list[idx1][1] != domain_end) chain[1] += 1;
if(chain[0] != chain[1]) nb_chains[i].push_back(chain); if(chain[0] != chain[1]) nb_chains[i].push_back(chain);
idx_s = (j == nnb - 1) ? -1 : nb_list[j + 1]; idx_s = (j == nnb - 1) ? -1 : nb_list[j + 1];

6
src/USER-CNT/cntlist.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -39,7 +39,7 @@ public:
const std::vector<array2003<int,2> >& get_segments() const; const std::vector<array2003<int,2> >& get_segments() const;
//list of triplets //list of triplets
const std::vector<array2003<int,3> >& get_triplets() const; const std::vector<array2003<int,3> >& get_triplets() const;
//list of neigbor chains [start,end] for segments //list of neigbor chains [start,end] for segments
//(use idx() to get real indexes) //(use idx() to get real indexes)
const std::vector<std::vector<array2003<int,2> > >& get_nbs() const; const std::vector<std::vector<array2003<int,2> > >& get_nbs() const;
//convert idx from sorted representation to real idx //convert idx from sorted representation to real idx
@ -67,7 +67,7 @@ private:
//============================================================================= //=============================================================================
inline const std::vector<std::vector<array2003<int, 2> > > & CNTList::get_nbs() inline const std::vector<std::vector<array2003<int, 2> > > & CNTList::get_nbs()
const { const {
return nb_chains; return nb_chains;
} }

2
src/USER-CNT/compute_cnt_B.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
src/USER-CNT/compute_cnt_B.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
src/USER-CNT/compute_cnt_Eb.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
src/USER-CNT/compute_cnt_Eb.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
src/USER-CNT/compute_cnt_Eb_tot.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
src/USER-CNT/compute_cnt_Eb_tot.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

4
src/USER-CNT/compute_cnt_Es.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -80,7 +80,7 @@ void ComputeCNT_Es::compute_peratom()
// clear local energy array // clear local energy array
for (i = 0; i < ntotal; i++) energy[i] = 0.0; for (i = 0; i < ntotal; i++) energy[i] = 0.0;
if (force->pair){ if (force->pair){
try { try {
PairCNTTPM* pair = dynamic_cast<PairCNTTPM*>(force->pair); PairCNTTPM* pair = dynamic_cast<PairCNTTPM*>(force->pair);

2
src/USER-CNT/compute_cnt_Es.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
src/USER-CNT/compute_cnt_Es_tot.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
src/USER-CNT/compute_cnt_Es_tot.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

4
src/USER-CNT/compute_cnt_Et.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -80,7 +80,7 @@ void ComputeCNT_Et::compute_peratom()
// clear local energy array // clear local energy array
for (i = 0; i < ntotal; i++) energy[i] = 0.0; for (i = 0; i < ntotal; i++) energy[i] = 0.0;
if (force->pair){ if (force->pair){
try { try {
PairCNTTPM* pair = dynamic_cast<PairCNTTPM*>(force->pair); PairCNTTPM* pair = dynamic_cast<PairCNTTPM*>(force->pair);

2
src/USER-CNT/compute_cnt_Et.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
src/USER-CNT/compute_cnt_Et_tot.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

2
src/USER-CNT/compute_cnt_Et_tot.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

18
src/USER-CNT/export_cnt.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -19,12 +19,12 @@ extern "C" {
// see ExportCNT.f90 in lib/cnt for function details // see ExportCNT.f90 in lib/cnt for function details
void TPBInit(); void TPBInit();
void TPMInit(const int& M, const int& N); void TPMInit(const int& M, const int& N);
void SetTablePath(const char* TPMSSTPFile, const int& N1, void SetTablePath(const char* TPMSSTPFile, const int& N1,
const char* TPMAFile, const int& N2); const char* TPMAFile, const int& N2);
void InitCNTPotModule(const int& STRModel, const int& STRParams, void InitCNTPotModule(const int& STRModel, const int& STRParams,
const int& YMType, const int& BNDModel, const double& Rref); const int& YMType, const int& BNDModel, const double& Rref);
double get_R(); double get_R();
void TubeStretchingForceField(double& U1, double& U2, double* F1, void TubeStretchingForceField(double& U1, double& U2, double* F1,
@ -32,17 +32,17 @@ extern "C" {
const double& R12, const double& L12); const double& R12, const double& L12);
void TubeBendingForceField(double& U1, double& U2, double& U3, double* F1, void TubeBendingForceField(double& U1, double& U2, double& U3, double* F1,
double* F2, double* F3, double* S1, double* S2, double* S3, double* F2, double* F3, double* S1, double* S2, double* S3,
const double* X1, const double* X2, const double* X3, const double& R123, const double* X1, const double* X2, const double* X3, const double& R123,
const double& L123, int& BBF2 ); const double& L123, int& BBF2 );
void SegmentTubeForceField(double& U1, double& U2, double *U, double* F1, void SegmentTubeForceField(double& U1, double& U2, double *U, double* F1,
double* F2, double* F, double* Fe, double* S1, double* S2, double* S, double* F2, double* F, double* Fe, double* S1, double* S2, double* S,
double* Se, const double* X1, const double* X2, const double& R12, double* Se, const double* X1, const double* X2, const double& R12,
const int& N, const double* X, const double* Xe, const int* BBF, const int& N, const double* X, const double* Xe, const int* BBF,
const double& R, const int& E1, const int& E2, const int& Ee, const double& R, const int& E1, const int& E2, const int& Ee,
const int& TPMType); const int& TPMType);
#ifdef __cplusplus #ifdef __cplusplus
} }
#endif #endif

20
src/USER-CNT/pair_cnt_tpm.cpp
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -47,7 +47,7 @@ PairCNTTPM::PairCNTTPM(LAMMPS *lmp) : Pair(lmp) {
TPMType = 0; // Inter-tube segment-segment interaction TPMType = 0; // Inter-tube segment-segment interaction
tab_path = NULL; tab_path = NULL;
tab_path_length = 0; tab_path_length = 0;
eatom_s = NULL; eatom_s = NULL;
eatom_b = NULL; eatom_b = NULL;
eatom_t = NULL; eatom_t = NULL;
@ -61,7 +61,7 @@ PairCNTTPM::~PairCNTTPM()
memory->destroy(setflag); memory->destroy(setflag);
memory->destroy(cutsq); memory->destroy(cutsq);
memory->destroy(cut); memory->destroy(cut);
memory->destroy(eatom_s); memory->destroy(eatom_s);
memory->destroy(eatom_b); memory->destroy(eatom_b);
memory->destroy(eatom_t); memory->destroy(eatom_t);
@ -153,7 +153,7 @@ void PairCNTTPM::compute(int eflag, int vflag){
double* S1 = &(s_sort[9*idx_s0]); double* S1 = &(s_sort[9*idx_s0]);
double* S2 = &(s_sort[9*idx_s1]); double* S2 = &(s_sort[9*idx_s1]);
double R12 = r[s[0]]; if (R12 > Rmax) Rmax = R12; double R12 = r[s[0]]; if (R12 > Rmax) Rmax = R12;
if (std::abs(R12 - RT) > 1e-3) if (std::abs(R12 - RT) > 1e-3)
error->all(FLERR,"Inconsistent input and potential table"); error->all(FLERR,"Inconsistent input and potential table");
//assume that the length of the segment is defined by the node with //assume that the length of the segment is defined by the node with
//smallest global id //smallest global id
@ -162,7 +162,7 @@ void PairCNTTPM::compute(int eflag, int vflag){
for (int nc = 0; nc < cntlist.get_nbs()[i].size(); nc++){ for (int nc = 0; nc < cntlist.get_nbs()[i].size(); nc++){
//id of the beginning and end of the chain in the sorted representation //id of the beginning and end of the chain in the sorted representation
const array2003<int,2>& chain = cntlist.get_nbs()[i][nc]; const array2003<int,2>& chain = cntlist.get_nbs()[i][nc];
int N = chain[1] - chain[0] + 1; //number of elements in the chain int N = chain[1] - chain[0] + 1; //number of elements in the chain
int end1 = cntlist.get_idx(chain[0]); //chain ends (real representation) int end1 = cntlist.get_idx(chain[0]); //chain ends (real representation)
int end2 = cntlist.get_idx(chain[1]); int end2 = cntlist.get_idx(chain[1]);
@ -178,8 +178,8 @@ void PairCNTTPM::compute(int eflag, int vflag){
int Ee = 0; int Ee = 0;
double* Xe = X; double* Fe = F; double* Se = S; double* Xe = X; double* Fe = F; double* Se = S;
if (!E1 && cntlist.get_triplet(end1)[0] != CNTList::domain_end && if (!E1 && cntlist.get_triplet(end1)[0] != CNTList::domain_end &&
cntlist.get_triplet(cntlist.get_triplet(end1)[0])[0] == cntlist.get_triplet(cntlist.get_triplet(end1)[0])[0] ==
CNTList::cnt_end){ CNTList::cnt_end){
Ee = 1; Ee = 1;
int idx = cntlist.get_idxb(cntlist.get_triplet(end1)[0]); int idx = cntlist.get_idxb(cntlist.get_triplet(end1)[0]);
@ -187,8 +187,8 @@ void PairCNTTPM::compute(int eflag, int vflag){
Fe = &(f_sort[3*idx]); Fe = &(f_sort[3*idx]);
Se = &(s_sort[9*idx]); Se = &(s_sort[9*idx]);
} }
else if (!E2 && cntlist.get_triplet(end2)[2] != CNTList::domain_end && else if (!E2 && cntlist.get_triplet(end2)[2] != CNTList::domain_end &&
cntlist.get_triplet(cntlist.get_triplet(end2)[2])[2] == cntlist.get_triplet(cntlist.get_triplet(end2)[2])[2] ==
CNTList::cnt_end){ CNTList::cnt_end){
Ee = 2; Ee = 2;
int idx = cntlist.get_idxb(cntlist.get_triplet(end2)[2]); int idx = cntlist.get_idxb(cntlist.get_triplet(end2)[2]);
@ -196,7 +196,7 @@ void PairCNTTPM::compute(int eflag, int vflag){
Fe = &(f_sort[3*idx]); Fe = &(f_sort[3*idx]);
Se = &(s_sort[9*idx]); Se = &(s_sort[9*idx]);
} }
SegmentTubeForceField(U1t, U2t, Ut, F1, F2, F, Fe, S1, S2, S, Se, X1, SegmentTubeForceField(U1t, U2t, Ut, F1, F2, F, Fe, S1, S2, S, Se, X1,
X2, R12, N, X, Xe, BBF, R, E1, E2, Ee, TPMType); X2, R12, N, X, Xe, BBF, R, E1, E2, Ee, TPMType);
} }

10
src/USER-CNT/pair_cnt_tpm.h
View File

@ -9,7 +9,7 @@
the GNU General Public License. the GNU General Public License.
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -46,15 +46,15 @@ class PairCNTTPM : public Pair {
double energy_b; // accumulated energies for bending double energy_b; // accumulated energies for bending
double energy_t; // accumulated energies for tube-tube interaction double energy_t; // accumulated energies for tube-tube interaction
double *eatom_s, *eatom_b, *eatom_t; // accumulated per-atom values double *eatom_s, *eatom_b, *eatom_t; // accumulated per-atom values
protected: protected:
int BendingMode, TPMType; int BendingMode, TPMType;
char* tab_path; char* tab_path;
int tab_path_length; int tab_path_length;
double cut_global; double cut_global;
double **cut; double **cut;
virtual void allocate(); virtual void allocate();
}; };
@ -91,7 +91,7 @@ Self-explanatory.
E: Inconsistent input and potential table E: Inconsistent input and potential table
The tube diameter is inconsistent with the chirality specified The tube diameter is inconsistent with the chirality specified
during generation of the potential table. during generation of the potential table.
*/ */

6
src/atom.cpp
View File

@ -109,7 +109,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
edpd_temp = edpd_flux = edpd_cv = NULL; edpd_temp = edpd_flux = edpd_cv = NULL;
// USER-CNT package // USER-CNT package
length = NULL; length = NULL;
buckling = NULL; buckling = NULL;
bond_cnt = NULL; bond_cnt = NULL;
@ -373,7 +373,7 @@ Atom::~Atom()
for (int i = 0; i < nmolecule; i++) delete molecules[i]; for (int i = 0; i < nmolecule; i++) delete molecules[i];
memory->sfree(molecules); memory->sfree(molecules);
// USER-CNT package // USER-CNT package
memory->destroy(length); memory->destroy(length);
memory->destroy(buckling); memory->destroy(buckling);
@ -2295,7 +2295,7 @@ void *Atom::extract(char *name)
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta; if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp; if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
// USER-CNT package // USER-CNT package
if (strcmp(name,"length") == 0) return (void *) length; if (strcmp(name,"length") == 0) return (void *) length;
if (strcmp(name,"buckling") == 0) return (void *) buckling; if (strcmp(name,"buckling") == 0) return (void *) buckling;