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zhi-wangzhi-wang
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sync with tinker8 that uses a condensed vdw matrix
1 parent 18e636a commit 25dfb82

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18 files changed

+160
-50
lines changed

18 files changed

+160
-50
lines changed

‎ext/interface/CMakeLists.txt‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -80,6 +80,7 @@ add_library (tinkerObjF OBJECT
8080
../source/kopdst.f
8181
../source/korbs.f
8282
../source/kpitor.f
83+
../source/kpolpr.f
8384
../source/kpolr.f
8485
../source/krepl.f
8586
../source/ksolut.f
@@ -352,6 +353,8 @@ add_library (tinkerObjF OBJECT
352353
../source/freeunit.f
353354
../source/geometry.f
354355
../source/getarc.f
356+
../source/getcart.f
357+
../source/getdcd.f
355358
../source/getint.f
356359
../source/getkey.f
357360
../source/getmol.f
@@ -461,6 +464,7 @@ add_library (tinkerObjF OBJECT
461464
../source/pressure.f
462465
../source/prmkey.f
463466
../source/promo.f
467+
../source/prtarc.f
464468
../source/prtdcd.f
465469
../source/prtdyn.f
466470
../source/prterr.f
@@ -474,6 +478,8 @@ add_library (tinkerObjF OBJECT
474478
../source/quatfit.f
475479
../source/random.f
476480
../source/rattle.f
481+
../source/readcart.f
482+
../source/readdcd.f
477483
../source/readdyn.f
478484
../source/readgau.f
479485
../source/readgdma.f

‎ext/interface/cpp/tinker/detail/expol.hh‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ extern double*& kpep;
88
extern double*& prepep;
99
extern double*& dmppep;
1010
extern double*& polscale;
11-
extern double*& invpolscale;
11+
extern double*& polinv;
1212
extern int*& lpep;
1313

1414
#ifdef TINKER_FORTRAN_MODULE_CPP
@@ -17,15 +17,15 @@ extern "C" double* TINKER_MOD(expol, kpep);
1717
extern "C" double* TINKER_MOD(expol, prepep);
1818
extern "C" double* TINKER_MOD(expol, dmppep);
1919
extern "C" double* TINKER_MOD(expol, polscale);
20-
extern "C" double* TINKER_MOD(expol, invpolscale);
20+
extern "C" double* TINKER_MOD(expol, polinv);
2121
extern "C" int* TINKER_MOD(expol, lpep);
2222

2323
int& nexpol = TINKER_MOD(expol, nexpol);
2424
double*& kpep = TINKER_MOD(expol, kpep);
2525
double*& prepep = TINKER_MOD(expol, prepep);
2626
double*& dmppep = TINKER_MOD(expol, dmppep);
2727
double*& polscale = TINKER_MOD(expol, polscale);
28-
double*& invpolscale = TINKER_MOD(expol, invpolscale);
28+
double*& polinv = TINKER_MOD(expol, polinv);
2929
int*& lpep = TINKER_MOD(expol, lpep);
3030
#endif
3131
} }

‎ext/interface/cpp/tinker/detail/inform.hh‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@
44

55
namespace tinker { namespace inform {
66
const int maxask = 5;
7+
extern int& gpucard;
78
extern int& digits;
89
extern int& iprint;
910
extern int& iwrite;
@@ -15,6 +16,7 @@ extern int& holdup;
1516
extern int& abort;
1617

1718
#ifdef TINKER_FORTRAN_MODULE_CPP
19+
extern "C" int TINKER_MOD(inform, gpucard);
1820
extern "C" int TINKER_MOD(inform, digits);
1921
extern "C" int TINKER_MOD(inform, iprint);
2022
extern "C" int TINKER_MOD(inform, iwrite);
@@ -25,6 +27,7 @@ extern "C" int TINKER_MOD(inform, silent);
2527
extern "C" int TINKER_MOD(inform, holdup);
2628
extern "C" int TINKER_MOD(inform, abort);
2729

30+
int& gpucard = TINKER_MOD(inform, gpucard);
2831
int& digits = TINKER_MOD(inform, digits);
2932
int& iprint = TINKER_MOD(inform, iprint);
3033
int& iwrite = TINKER_MOD(inform, iwrite);

‎ext/interface/cpp/tinker/detail/kpolpr.hh‎

Lines changed: 22 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,22 @@
1+
#pragma once
2+
3+
#include "macro.hh"
4+
5+
namespace tinker { namespace kpolpr {
6+
extern int& maxnpp;
7+
extern double*& thlpr;
8+
extern double*& thdpr;
9+
extern char (*&kppr)[8];
10+
11+
#ifdef TINKER_FORTRAN_MODULE_CPP
12+
extern "C" int TINKER_MOD(kpolpr, maxnpp);
13+
extern "C" double* TINKER_MOD(kpolpr, thlpr);
14+
extern "C" double* TINKER_MOD(kpolpr, thdpr);
15+
extern "C" char (*TINKER_MOD(kpolpr, kppr))[8];
16+
17+
int& maxnpp = TINKER_MOD(kpolpr, maxnpp);
18+
double*& thlpr = TINKER_MOD(kpolpr, thlpr);
19+
double*& thdpr = TINKER_MOD(kpolpr, thdpr);
20+
char (*&kppr)[8] = TINKER_MOD(kpolpr, kppr);
21+
#endif
22+
} }

‎ext/interface/cpp/tinker/detail/kpolr.hh‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,17 +6,17 @@ namespace tinker { namespace kpolr {
66
extern int*& pgrp;
77
extern double*& polr;
88
extern double*& athl;
9-
extern double*& ddir;
9+
extern double*& dthl;
1010

1111
#ifdef TINKER_FORTRAN_MODULE_CPP
1212
extern "C" int* TINKER_MOD(kpolr, pgrp);
1313
extern "C" double* TINKER_MOD(kpolr, polr);
1414
extern "C" double* TINKER_MOD(kpolr, athl);
15-
extern "C" double* TINKER_MOD(kpolr, ddir);
15+
extern "C" double* TINKER_MOD(kpolr, dthl);
1616

1717
int*& pgrp = TINKER_MOD(kpolr, pgrp);
1818
double*& polr = TINKER_MOD(kpolr, polr);
1919
double*& athl = TINKER_MOD(kpolr, athl);
20-
double*& ddir = TINKER_MOD(kpolr, ddir);
20+
double*& dthl = TINKER_MOD(kpolr, dthl);
2121
#endif
2222
} }

‎ext/interface/cpp/tinker/detail/output.hh‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,8 @@ extern int& binary;
88
extern int& noversion;
99
extern int& overwrite;
1010
extern int& cyclesave;
11+
extern int& arcsave;
12+
extern int& dcdsave;
1113
extern int& velsave;
1214
extern int& frcsave;
1315
extern int& uindsave;
@@ -19,6 +21,8 @@ extern "C" int TINKER_MOD(output, binary);
1921
extern "C" int TINKER_MOD(output, noversion);
2022
extern "C" int TINKER_MOD(output, overwrite);
2123
extern "C" int TINKER_MOD(output, cyclesave);
24+
extern "C" int TINKER_MOD(output, arcsave);
25+
extern "C" int TINKER_MOD(output, dcdsave);
2226
extern "C" int TINKER_MOD(output, velsave);
2327
extern "C" int TINKER_MOD(output, frcsave);
2428
extern "C" int TINKER_MOD(output, uindsave);
@@ -29,6 +33,8 @@ int& binary = TINKER_MOD(output, binary);
2933
int& noversion = TINKER_MOD(output, noversion);
3034
int& overwrite = TINKER_MOD(output, overwrite);
3135
int& cyclesave = TINKER_MOD(output, cyclesave);
36+
int& arcsave = TINKER_MOD(output, arcsave);
37+
int& dcdsave = TINKER_MOD(output, dcdsave);
3238
int& velsave = TINKER_MOD(output, velsave);
3339
int& frcsave = TINKER_MOD(output, frcsave);
3440
int& uindsave = TINKER_MOD(output, uindsave);

‎ext/interface/cpp/tinker/detail/polar.hh‎

Lines changed: 12 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -5,10 +5,13 @@
55
namespace tinker { namespace polar {
66
extern int& npolar;
77
extern int*& ipolar;
8+
extern int*& jpolar;
89
extern double*& polarity;
910
extern double*& thole;
10-
extern double*& dirdamp;
11+
extern double*& tholed;
1112
extern double*& pdamp;
13+
extern double*& thlval;
14+
extern double*& thdval;
1215
extern double*& udir;
1316
extern double*& udirp;
1417
extern double*& udirs;
@@ -23,10 +26,13 @@ extern int*& douind;
2326
#ifdef TINKER_FORTRAN_MODULE_CPP
2427
extern "C" int TINKER_MOD(polar, npolar);
2528
extern "C" int* TINKER_MOD(polar, ipolar);
29+
extern "C" int* TINKER_MOD(polar, jpolar);
2630
extern "C" double* TINKER_MOD(polar, polarity);
2731
extern "C" double* TINKER_MOD(polar, thole);
28-
extern "C" double* TINKER_MOD(polar, dirdamp);
32+
extern "C" double* TINKER_MOD(polar, tholed);
2933
extern "C" double* TINKER_MOD(polar, pdamp);
34+
extern "C" double* TINKER_MOD(polar, thlval);
35+
extern "C" double* TINKER_MOD(polar, thdval);
3036
extern "C" double* TINKER_MOD(polar, udir);
3137
extern "C" double* TINKER_MOD(polar, udirp);
3238
extern "C" double* TINKER_MOD(polar, udirs);
@@ -40,10 +46,13 @@ extern "C" int* TINKER_MOD(polar, douind);
4046

4147
int& npolar = TINKER_MOD(polar, npolar);
4248
int*& ipolar = TINKER_MOD(polar, ipolar);
49+
int*& jpolar = TINKER_MOD(polar, jpolar);
4350
double*& polarity = TINKER_MOD(polar, polarity);
4451
double*& thole = TINKER_MOD(polar, thole);
45-
double*& dirdamp = TINKER_MOD(polar, dirdamp);
52+
double*& tholed = TINKER_MOD(polar, tholed);
4653
double*& pdamp = TINKER_MOD(polar, pdamp);
54+
double*& thlval = TINKER_MOD(polar, thlval);
55+
double*& thdval = TINKER_MOD(polar, thdval);
4756
double*& udir = TINKER_MOD(polar, udir);
4857
double*& udirp = TINKER_MOD(polar, udirp);
4958
double*& udirs = TINKER_MOD(polar, udirs);

‎ext/interface/cpp/tinker/detail/polpot.hh‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@ extern double& uaccel;
2929
extern int& polprt;
3030
extern int& dpequal;
3131
extern int& use_thole;
32-
extern int& use_dirdamp;
32+
extern int& use_tholed;
3333
extern int& use_expol;
3434
extern char (&scrtyp)[3];
3535
extern char (&poltyp)[6];
@@ -61,7 +61,7 @@ extern "C" double TINKER_MOD(polpot, uaccel);
6161
extern "C" int TINKER_MOD(polpot, polprt);
6262
extern "C" int TINKER_MOD(polpot, dpequal);
6363
extern "C" int TINKER_MOD(polpot, use_thole);
64-
extern "C" int TINKER_MOD(polpot, use_dirdamp);
64+
extern "C" int TINKER_MOD(polpot, use_tholed);
6565
extern "C" int TINKER_MOD(polpot, use_expol);
6666
extern "C" char TINKER_MOD(polpot, scrtyp)[3];
6767
extern "C" char TINKER_MOD(polpot, poltyp)[6];
@@ -92,7 +92,7 @@ double& uaccel = TINKER_MOD(polpot, uaccel);
9292
int& polprt = TINKER_MOD(polpot, polprt);
9393
int& dpequal = TINKER_MOD(polpot, dpequal);
9494
int& use_thole = TINKER_MOD(polpot, use_thole);
95-
int& use_dirdamp = TINKER_MOD(polpot, use_dirdamp);
95+
int& use_tholed = TINKER_MOD(polpot, use_tholed);
9696
int& use_expol = TINKER_MOD(polpot, use_expol);
9797
char (&scrtyp)[3] = TINKER_MOD(polpot, scrtyp);
9898
char (&poltyp)[6] = TINKER_MOD(polpot, poltyp);

‎ext/interface/cpp/tinker/modcpp.h‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -76,6 +76,7 @@
7676
#include "detail/kopdst.hh"
7777
#include "detail/korbs.hh"
7878
#include "detail/kpitor.hh"
79+
#include "detail/kpolpr.hh"
7980
#include "detail/kpolr.hh"
8081
#include "detail/krepl.hh"
8182
#include "detail/ksolut.hh"

‎ext/interface/cpp/tinker/routines.h‎

Lines changed: 29 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@ void altpol0a_();
3636
#define tinker_f_altpol0a altpol0a_
3737
void altpol0b_();
3838
#define tinker_f_altpol0b altpol0b_
39-
void rotexpl_(double* xr, double* yr, double* zr, double* p33i, double* p33k, double* ks2i, double* ks2k);
39+
void rotexpl_(double* r, double* xr, double* yr, double* zr, double* p33i, double* p33k, double* ks2i, double* ks2k);
4040
#define tinker_f_rotexpl rotexpl_
4141

4242
// analysis.f
@@ -236,8 +236,8 @@ void dampewald_(int* rorder, double* r, double* r2, double* scale, double* dmpe)
236236
#define tinker_f_dampewald dampewald_
237237
void dampthole_(int* i, int* k, int* rorder, double* r, double* dmpik);
238238
#define tinker_f_dampthole dampthole_
239-
void dampthole2_(int* i, int* k, int* rorder, double* r, double* dmpik);
240-
#define tinker_f_dampthole2 dampthole2_
239+
void damptholed_(int* i, int* k, int* rorder, double* r, double* dmpik);
240+
#define tinker_f_damptholed damptholed_
241241
void damppole_(double* r, int* rorder, double* alphai, double* alphak, double* dmpi, double* dmpk, double* dmpik);
242242
#define tinker_f_damppole damppole_
243243
void dampdir_(double* r, double* alphai, double* alphak, double* dmpi, double* dmpk);
@@ -270,7 +270,7 @@ void dexpol1a_();
270270
#define tinker_f_dexpol1a dexpol1a_
271271
void dexpol1b_();
272272
#define tinker_f_dexpol1b dexpol1b_
273-
void rotdexpl_(double* xr, double* yr, double* zr, double* ai, double* ak);
273+
void rotdexpl_(double* r, double* xr, double* yr, double* zr, double* ai, double* ak);
274274
#define tinker_f_rotdexpl rotdexpl_
275275

276276
// diagq.f
@@ -1431,6 +1431,14 @@ double geometry_(int* ia, int* ib, int* ic, int* id);
14311431
void getarc_(int* iarc);
14321432
#define tinker_f_getarc getarc_
14331433

1434+
// getcart.f
1435+
void getcart_(int* ixyz);
1436+
#define tinker_f_getcart getcart_
1437+
1438+
// getdcd.f
1439+
void getdcd_(int* idcd);
1440+
#define tinker_f_getdcd getdcd_
1441+
14341442
// getint.f
14351443
void getint_();
14361444
#define tinker_f_getint getint_
@@ -2145,8 +2153,16 @@ void nbondoff_();
21452153
void promo_();
21462154
#define tinker_f_promo promo_
21472155

2156+
// prtarc.f
2157+
void prtarc_(int* iarc, int* first);
2158+
#define tinker_f_prtarc prtarc_
2159+
void prtarcf_(int* iarc);
2160+
#define tinker_f_prtarcf prtarcf_
2161+
void prtarcb_(int* idcd, int* first);
2162+
#define tinker_f_prtarcb prtarcb_
2163+
21482164
// prtdcd.f
2149-
void prtdcd_(int* idcd);
2165+
void prtdcd_(int* idcd, int* first);
21502166
#define tinker_f_prtdcd prtdcd_
21512167

21522168
// prtdyn.f
@@ -2215,6 +2231,14 @@ void shake_(double* xold, double* yold, double* zold);
22152231
void shake2_(double* derivs);
22162232
#define tinker_f_shake2 shake2_
22172233

2234+
// readcart.f
2235+
void readcart_(int* ixyz, int* first);
2236+
#define tinker_f_readcart readcart_
2237+
2238+
// readdcd.f
2239+
void readdcd_(int* idcd, int* first);
2240+
#define tinker_f_readdcd readdcd_
2241+
22182242
// readdyn.f
22192243
void readdyn_(int* idyn);
22202244
#define tinker_f_readdyn readdyn_

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