forked from plumed/plumed2
-
Notifications
You must be signed in to change notification settings - Fork 0
/
namd-2.8.diff
266 lines (252 loc) · 7.37 KB
/
namd-2.8.diff
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
patch -u -l -b -F 5 --suffix=.preplumed "./Makefile" << \EOF_EOF
--- ./Makefile.preplumed
+++ ./Makefile
@@ -358,10 +358,12 @@
cat $(BUILDINFO).C; \
$(CXX) $(CXXFLAGS) $(COPTO)$(BUILDINFO).o $(COPTC) $(BUILDINFO).C
all: $(BINARIES) $(LIBCUDARTSO)
+include .rootdir/Plumed.inc
+
namd2: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
$(MAKEBUILDINFO)
$(CHARMC) -verbose -ld++-option \
"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
-module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -language charm++ \
@@ -371,10 +373,11 @@
$(CUDALIB) \
$(DPMTALIB) \
$(DPMELIB) \
$(TCLLIB) \
$(FFTLIB) \
+ $(PLUMED_LOAD) \
$(PLUGINLIB) \
$(CHARMOPTS) \
$(EXTRALINKLIBS) \
-lm -o namd2
EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
--- ./src/ComputeMgr.C.preplumed
+++ ./src/ComputeMgr.C
@@ -77,13 +77,137 @@
#include "GlobalMasterSMD.h"
#include "GlobalMasterTMD.h"
#include "GlobalMasterSymmetry.h"
#include "GlobalMasterEasy.h"
#include "GlobalMasterMisc.h"
+// PLUMED
+#include "../Plumed.h"
+// END PLUMED
#include "GlobalMasterFreeEnergy.h"
#include "GlobalMasterColvars.h"
+class GlobalMasterPlumed:
+ public GlobalMasterEasy,
+ private PLMD::Plumed
+{
+ std::vector<int> index;
+ std::vector<double> positions;
+ std::vector<double> forces;
+ std::vector<double> masses;
+ std::vector<double> charges;
+ double box[3][3];
+ SimParameters *spar;
+public:
+ GlobalMasterPlumed():
+ GlobalMasterEasy("plumedScript")
+ {
+ easy_init(config);
+ }
+ void easy_init(const char* config)
+ {
+ int realPrecision=sizeof(double);
+ cmd("setRealPrecision",&realPrecision);
+ spar=Node::Object()->simParameters;
+
+ double energyUnits=4.184;
+ double lengthUnits=0.1;
+ double timeUnits=0.001;
+ cmd("setMDEnergyUnits",&energyUnits);
+ cmd("setMDLengthUnits",&lengthUnits);
+ cmd("setMDTimeUnits",&timeUnits);
+
+ cmd("setPlumedDat",spar->plumedFilename);
+
+ int natoms=Node::Object()->molecule->numAtoms;
+ cmd("setNatoms",&natoms);
+
+ cmd("setMDEngine","namd");
+
+ cmd("setLog",stdout);
+
+ double dt=spar->dt;
+ cmd("setTimestep",&dt);
+ cmd("setNoVirial");
+ cmd("init");
+
+ int s=step+1;
+ cmd("setStep",&s);
+ share();
+
+ }
+
+ void share(){
+ int* p;
+ int n;
+ bool redo=false;
+ cmd("prepareDependencies");
+ cmd("createFullList",&n);
+ cmd("getFullList",&p);
+ if(index.size()!=n)redo=true;
+ if(!redo) for(int i=0;i<n;i++) if(index[i]!=p[i]) { redo=true; break;};
+ if(redo){
+ index.resize(n);
+ masses.resize(n);
+ modifyRequestedAtoms().resize(0);
+ for(int i=0;i<n;i++){
+ requestAtom(p[i]);
+ masses[i]=getMass(p[i]);
+ index[i]=p[i];
+ };
+ positions.resize(3*n);
+ forces.resize(3*n);
+ charges.resize(n);
+
+ cmd("setAtomsNlocal",&n);
+ cmd("setAtomsGatindex",&index[0]);
+ }
+ cmd("clearFullList");
+ }
+
+ void easy_calc(){
+
+ for(int i=0;i<index.size();i++){
+ Vector coord;
+ getPosition(index[i],coord);
+ positions[3*i+0]=coord.x;
+ positions[3*i+1]=coord.y;
+ positions[3*i+2]=coord.z;
+ masses[i]=Node::Object()->molecule->atommass(i);
+ charges[i]=Node::Object()->molecule->atommass(i);
+ };
+
+ if(spar->lattice.volume()>0.0){
+ for(int i=0;i<3;i++) box[0][i]=spar->lattice.a()[i];
+ for(int i=0;i<3;i++) box[1][i]=spar->lattice.b()[i];
+ for(int i=0;i<3;i++) box[2][i]=spar->lattice.c()[i];
+ cmd("setBox",&box[0][0]);
+ }
+
+ for(int i=0;i<forces.size();i++) forces[i]=0.0;
+
+ cmd("setMasses",&masses[0]);
+ cmd("setPositions",&positions[0]);
+ cmd("setForces",&forces[0]);
+
+ cmd("shareData");
+ cmd("performCalc");
+
+ for(int i=0;i<index.size();i++){
+ Vector f;
+ f.x=forces[3*i+0];
+ f.y=forces[3*i+1];
+ f.z=forces[3*i+2];
+ int j=addForce(index[i],f);
+ };
+
+ int s=step+1;
+ cmd("setStep",&s);
+ share();
+
+ }
+};
+
ComputeMgr::ComputeMgr()
{
CkpvAccess(BOCclass_group).computeMgr = thisgroup;
computeGlobalObject = 0;
computeDPMEObject = 0;
@@ -743,10 +867,15 @@
masterServerObject->addClient(new GlobalMasterSymmetry());
if (simParams->TMDOn)
masterServerObject->addClient(new GlobalMasterTMD());
if (simParams->miscForcesOn)
masterServerObject->addClient(new GlobalMasterMisc());
+ // PLUMED
+ if (simParams->plumedOn){
+ masterServerObject->addClient(new GlobalMasterPlumed());
+ }
+ // END PLUMED
if ( simParams->freeEnergyOn )
masterServerObject->addClient(new GlobalMasterFreeEnergy());
if ( simParams->colvarsOn )
masterServerObject->addClient(new GlobalMasterColvars());
EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
--- ./src/SimParameters.C.preplumed
+++ ./src/SimParameters.C
@@ -1231,10 +1231,17 @@
opts.optionalB("main", "GBIS", "Use GB implicit solvent?",
&GBISOn, FALSE);
opts.optionalB("main", "GBISSer", "Use GB implicit solvent?",
&GBISserOn, FALSE);
+
+ // PLUMED
+ //// plumed
+ opts.optionalB("main", "plumed", "Is PLUMED active?",&plumedOn,FALSE);
+ opts.require("plumed", "plumedfile","PLUMED script",PARSE_STRING);
+ // END PLUMED
+
opts.optional("GBIS", "solventDielectric",
"Solvent Dielectric", &solvent_dielectric, 78.5);
opts.optional("GBIS", "intrinsicRadiusOffset",
"Coulomb Radius Offset", &coulomb_radius_offset, 0.09);
opts.optional("GBIS", "ionConcentration",
@@ -4103,11 +4110,11 @@
}
// Global forces configuration
globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
- (IMDon) || SMDOn || TMDOn || colvarsOn || symmetryOn );
+ (IMDon) || SMDOn || TMDOn || colvarsOn || symmetryOn || plumedOn );
if (tclForcesOn)
{
iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";
@@ -4188,10 +4195,25 @@
}
iout << endi;
}
+ // PLUMED
+ if (plumedOn)
+ {
+ iout << iINFO << "PLUMED ACTIVE\n";
+
+ current = config->find("plumedfile");
+ iout << iINFO << "PLUMED CONFIG FILE "<< current->data << "\n" << endi;
+ strcpy(plumedFilename,current->data);
+
+ ifstream plumedFile(current->data);
+ if ( ! plumedFile ) NAMD_die("Error reading PLUMED config file.\n");
+
+ }
+ // END PLUMED
+
if (IMDon)
{
iout << iINFO << "INTERACTIVE MD ACTIVE\n";
iout << iINFO << "INTERACTIVE MD PORT " << IMDport << "\n";
iout << iINFO << "INTERACTIVE MD FREQ " << IMDfreq << "\n";
EOF_EOF
patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF
--- ./src/SimParameters.h.preplumed
+++ ./src/SimParameters.h
@@ -401,10 +401,13 @@
char tclBCArgs[128]; // Extra args for calcforces command
Bool freeEnergyOn; // Doing free energy perturbation?
Bool miscForcesOn; // Using misc forces?
Bool colvarsOn; // Using the colvars module?
+ Bool plumedOn; // Using Plumed?
+ char plumedFilename[1024]; // Plumed filename
+
Bool fixedAtomsOn; // Are there fixed atoms?
Bool fixedAtomsForces; // Calculate forces anyway?
Bool langevinOn; // Flag TRUE-> langevin dynamics active
BigReal langevinTemp; // Temperature for Langevin dynamics
EOF_EOF